# Librerias a utilizar
library("Biobase") # Funciones base de Bioconductor
library("biomaRt") # Acceso a bases de datos de Biomart
library("tidyverse") # Set de paquetes que hacen muchas cosas
library("magrittr") # Operadores cañeria (pipes) %>%
library("purrr") # Programación funcional (de funciones)
library("stringr") # Operadores consistentes para strings# Descargando objetos GEO a utilizar
data <- GEOquery::getGEO('GSE148349', # Un estudio con 66 datasets
GSEMatrix = TRUE, # Usa GSE como matrices, más eficiente
AnnotGPL = TRUE, # Pide anotaciones
getGPL = TRUE) # Plataforma utilizada
# Es objeto "data" es una lista de objetos.
class(data)## [1] "list"## $`GSE148349-GPL24247_series_matrix.txt.gz`
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 0 features, 40 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: GSM4462240 GSM4462241 ... GSM4462294 (40 total)
## varLabels: title geo_accession ... treatment/method:ch1 (46 total)
## varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation: GPL24247
##
## $`GSE148349-GPL24676_series_matrix.txt.gz`
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 0 features, 26 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: GSM4462262 GSM4462263 ... GSM4462305 (26 total)
## varLabels: title geo_accession ... treatment/method:ch1 (45 total)
## varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation: GPL24676## [1] "GSE148349-GPL24247_series_matrix.txt.gz"
## [2] "GSE148349-GPL24676_series_matrix.txt.gz"Los nombres de los datasets son algo complicados y verbosos, pero podemos usar funciones para simplificarlos.
# Primero hacemos nuevos nombres, que quedan en una lista
data %>% names %>% str_replace('_.*gz','') -> new.names
# Luego los aplicamos con el pipe boomerang
data %<>% purrr::set_names(new.names)
data %>% names # nombres algo más legibles## [1] "GSE148349-GPL24247" "GSE148349-GPL24676"Una base de las programación funcional son funciones que aplican funciones. Estas en general tienen mejor desempeño que loops e iteraciones, lo que las hace utiles para procesos que reutilizan un mismo flujo de trabajo a partir de data relativamente estandarizada. En R existen varios métodos, como lapply() dentro de las funciones base, o map() dentro del paquete purrr.
# ListApply aplica una función a cada objeto de una lista
lapply(data, slotNames) # en este caso, pregunta nombres## $`GSE148349-GPL24247`
## [1] "experimentData" "assayData" "phenoData"
## [4] "featureData" "annotation" "protocolData"
## [7] ".__classVersion__"
##
## $`GSE148349-GPL24676`
## [1] "experimentData" "assayData" "phenoData"
## [4] "featureData" "annotation" "protocolData"
## [7] ".__classVersion__"# Alternativamente, podemos usar map (de purrr)
# con la diferencia de que puede aplicar a vectores
# y usando variantes map_if() podemos hacerlo selectiva
purrr::map(data, slotNames)## $`GSE148349-GPL24247`
## [1] "experimentData" "assayData" "phenoData"
## [4] "featureData" "annotation" "protocolData"
## [7] ".__classVersion__"
##
## $`GSE148349-GPL24676`
## [1] "experimentData" "assayData" "phenoData"
## [4] "featureData" "annotation" "protocolData"
## [7] ".__classVersion__"# Y usar una función de Biobase para extraer fenotipos
# (si no funciona usamos lapply() en lugar de map())
purrr::map(data, pData)## $`GSE148349-GPL24247`
## title geo_accession
## GSM4462240 Untreated [p3138_5721/1] GSM4462240
## GSM4462241 Untreated [p3138_5721/2] GSM4462241
## GSM4462242 Untreated [p3138_5721/3] GSM4462242
## GSM4462243 Untreated [p3138_5721/4] GSM4462243
## GSM4462244 1 m after LNP injection [p3138_5721/5] GSM4462244
## GSM4462245 1 m after LNP injection [p3138_5721/6] GSM4462245
## GSM4462246 1 m after LNP injection [p3138_5721/7] GSM4462246
## GSM4462247 1 m after LNP injection [p3138_5721/8] GSM4462247
## GSM4462248 16 m after AAV injection, no sgRNA [p3138_5721/9] GSM4462248
## GSM4462249 16 m after AAV injection, no sgRNA [p3138_5721/10] GSM4462249
## GSM4462250 16 m after AAV injection, no sgRNA [p3138_5721/11] GSM4462250
## GSM4462251 16 m after AAV injection [p3138_5721/12] GSM4462251
## GSM4462252 16 m after AAV injection [p3138_5721/13] GSM4462252
## GSM4462253 16 m after AAV injection [p3138_5721/14] GSM4462253
## GSM4462254 16 m after AAV injection [p3138_5721/15] GSM4462254
## GSM4462255 48 h after LNP injection [p3138_5721/16] GSM4462255
## GSM4462256 48 h after LNP injection [p3138_5721/17] GSM4462256
## GSM4462257 48 h after LNP injection [p3138_5721/18] GSM4462257
## GSM4462258 48 h after LNP injection [p3138_5721/19] GSM4462258
## GSM4462259 2 m after AAV injection [p3138_5721/20] GSM4462259
## GSM4462260 2 m after AAV injection [p3138_5721/21] GSM4462260
## GSM4462261 2 m after AAV injection [p3138_5721/22] GSM4462261
## GSM4462277 4_rep1 [p3138_o6708/1] GSM4462277
## GSM4462278 2_rep1 [p3138_o6708/2] GSM4462278
## GSM4462279 1_rep1 [p3138_o6708/3] GSM4462279
## GSM4462280 0_5_rep1 [p3138_o6708/4] GSM4462280
## GSM4462281 0_25_rep1 [p3138_o6708/5] GSM4462281
## GSM4462282 0_rep1 [p3138_o6708/6] GSM4462282
## GSM4462283 4_rep2 [p3138_o6708/7] GSM4462283
## GSM4462284 2_rep2 [p3138_o6708/8] GSM4462284
## GSM4462285 1_rep2 [p3138_o6708/9] GSM4462285
## GSM4462286 0_5_rep2 [p3138_o6708/10] GSM4462286
## GSM4462287 0_25_rep2 [p3138_o6708/11] GSM4462287
## GSM4462288 0_rep2 [p3138_o6708/12] GSM4462288
## GSM4462289 4_rep3 [p3138_o6708/13] GSM4462289
## GSM4462290 2_rep3 [p3138_o6708/14] GSM4462290
## GSM4462291 1_rep3 [p3138_o6708/15] GSM4462291
## GSM4462292 0_5_rep3 [p3138_o6708/16] GSM4462292
## GSM4462293 0_25_rep3 [p3138_o6708/17] GSM4462293
## GSM4462294 0_rep3 [p3138_o6708/18] GSM4462294
## status submission_date last_update_date type
## GSM4462240 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462241 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462242 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462243 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462244 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462245 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462246 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462247 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462248 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462249 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462250 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462251 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462252 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462253 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462254 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462255 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462256 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462257 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462258 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462259 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462260 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462261 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462277 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462278 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462279 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462280 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462281 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462282 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462283 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462284 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462285 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462286 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462287 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462288 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462289 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462290 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462291 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462292 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462293 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462294 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## channel_count source_name_ch1
## GSM4462240 1 Pah-enu2_Untreated
## GSM4462241 1 Pah-enu2_Untreated
## GSM4462242 1 Pah-enu2_Untreated
## GSM4462243 1 Pah-enu2_Untreated
## GSM4462244 1 Pah-enu2_1 m after LNP injection
## GSM4462245 1 Pah-enu2_1 m after LNP injection
## GSM4462246 1 Pah-enu2_1 m after LNP injection
## GSM4462247 1 Pah-enu2_1 m after LNP injection
## GSM4462248 1 Pah-enu2_16 m after AAV injection, no sgRNA
## GSM4462249 1 Pah-enu2_16 m after AAV injection, no sgRNA
## GSM4462250 1 Pah-enu2_16 m after AAV injection, no sgRNA
## GSM4462251 1 Pah-enu2_16 m after AAV injection
## GSM4462252 1 Pah-enu2_16 m after AAV injection
## GSM4462253 1 Pah-enu2_16 m after AAV injection
## GSM4462254 1 Pah-enu2_16 m after AAV injection
## GSM4462255 1 Pah-enu2_48 h after LNP injection
## GSM4462256 1 Pah-enu2_48 h after LNP injection
## GSM4462257 1 Pah-enu2_48 h after LNP injection
## GSM4462258 1 Pah-enu2_48 h after LNP injection
## GSM4462259 1 Pah-enu2_2 m after AAV injection
## GSM4462260 1 Pah-enu2_2 m after AAV injection
## GSM4462261 1 Pah-enu2_2 m after AAV injection
## GSM4462277 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462278 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462279 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462280 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462281 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462282 1 Hepa1-6_RFP_48h
## GSM4462283 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462284 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462285 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462286 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462287 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462288 1 Hepa1-6_RFP_48h
## GSM4462289 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462290 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462291 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462292 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462293 1 Hepa1-6_saKKH-CBE3 + RFP_48h
## GSM4462294 1 Hepa1-6_RFP_48h
## organism_ch1 characteristics_ch1
## GSM4462240 Mus musculus cell line/strain: Pah-enu2
## GSM4462241 Mus musculus cell line/strain: Pah-enu2
## GSM4462242 Mus musculus cell line/strain: Pah-enu2
## GSM4462243 Mus musculus cell line/strain: Pah-enu2
## GSM4462244 Mus musculus cell line/strain: Pah-enu2
## GSM4462245 Mus musculus cell line/strain: Pah-enu2
## GSM4462246 Mus musculus cell line/strain: Pah-enu2
## GSM4462247 Mus musculus cell line/strain: Pah-enu2
## GSM4462248 Mus musculus cell line/strain: Pah-enu2
## GSM4462249 Mus musculus cell line/strain: Pah-enu2
## GSM4462250 Mus musculus cell line/strain: Pah-enu2
## GSM4462251 Mus musculus cell line/strain: Pah-enu2
## GSM4462252 Mus musculus cell line/strain: Pah-enu2
## GSM4462253 Mus musculus cell line/strain: Pah-enu2
## GSM4462254 Mus musculus cell line/strain: Pah-enu2
## GSM4462255 Mus musculus cell line/strain: Pah-enu2
## GSM4462256 Mus musculus cell line/strain: Pah-enu2
## GSM4462257 Mus musculus cell line/strain: Pah-enu2
## GSM4462258 Mus musculus cell line/strain: Pah-enu2
## GSM4462259 Mus musculus cell line/strain: Pah-enu2
## GSM4462260 Mus musculus cell line/strain: Pah-enu2
## GSM4462261 Mus musculus cell line/strain: Pah-enu2
## GSM4462277 Mus musculus cell line/strain: Hepa1-6
## GSM4462278 Mus musculus cell line/strain: Hepa1-6
## GSM4462279 Mus musculus cell line/strain: Hepa1-6
## GSM4462280 Mus musculus cell line/strain: Hepa1-6
## GSM4462281 Mus musculus cell line/strain: Hepa1-6
## GSM4462282 Mus musculus cell line/strain: Hepa1-6
## GSM4462283 Mus musculus cell line/strain: Hepa1-6
## GSM4462284 Mus musculus cell line/strain: Hepa1-6
## GSM4462285 Mus musculus cell line/strain: Hepa1-6
## GSM4462286 Mus musculus cell line/strain: Hepa1-6
## GSM4462287 Mus musculus cell line/strain: Hepa1-6
## GSM4462288 Mus musculus cell line/strain: Hepa1-6
## GSM4462289 Mus musculus cell line/strain: Hepa1-6
## GSM4462290 Mus musculus cell line/strain: Hepa1-6
## GSM4462291 Mus musculus cell line/strain: Hepa1-6
## GSM4462292 Mus musculus cell line/strain: Hepa1-6
## GSM4462293 Mus musculus cell line/strain: Hepa1-6
## GSM4462294 Mus musculus cell line/strain: Hepa1-6
## characteristics_ch1.1 characteristics_ch1.2
## GSM4462240 cell/sample type: Liver time point: 0
## GSM4462241 cell/sample type: Liver time point: 0
## GSM4462242 cell/sample type: Liver time point: 0
## GSM4462243 cell/sample type: Liver time point: 0
## GSM4462244 cell/sample type: Liver time point: 1m
## GSM4462245 cell/sample type: Liver time point: 1m
## GSM4462246 cell/sample type: Liver time point: 1m
## GSM4462247 cell/sample type: Liver time point: 1m
## GSM4462248 cell/sample type: Liver time point: 16m
## GSM4462249 cell/sample type: Liver time point: 16m
## GSM4462250 cell/sample type: Liver time point: 16m
## GSM4462251 cell/sample type: Liver time point: 16m
## GSM4462252 cell/sample type: Liver time point: 16m
## GSM4462253 cell/sample type: Liver time point: 16m
## GSM4462254 cell/sample type: Liver time point: 16m
## GSM4462255 cell/sample type: Liver time point: 48h
## GSM4462256 cell/sample type: Liver time point: 48h
## GSM4462257 cell/sample type: Liver time point: 48h
## GSM4462258 cell/sample type: Liver time point: 48h
## GSM4462259 cell/sample type: Liver time point: 2m
## GSM4462260 cell/sample type: Liver time point: 2m
## GSM4462261 cell/sample type: Liver time point: 2m
## GSM4462277 cell/sample type: cell lysate time point: 48h
## GSM4462278 cell/sample type: cell lysate time point: 48h
## GSM4462279 cell/sample type: cell lysate time point: 48h
## GSM4462280 cell/sample type: cell lysate time point: 48h
## GSM4462281 cell/sample type: cell lysate time point: 48h
## GSM4462282 cell/sample type: cell lysate time point: 48h
## GSM4462283 cell/sample type: cell lysate time point: 48h
## GSM4462284 cell/sample type: cell lysate time point: 48h
## GSM4462285 cell/sample type: cell lysate time point: 48h
## GSM4462286 cell/sample type: cell lysate time point: 48h
## GSM4462287 cell/sample type: cell lysate time point: 48h
## GSM4462288 cell/sample type: cell lysate time point: 48h
## GSM4462289 cell/sample type: cell lysate time point: 48h
## GSM4462290 cell/sample type: cell lysate time point: 48h
## GSM4462291 cell/sample type: cell lysate time point: 48h
## GSM4462292 cell/sample type: cell lysate time point: 48h
## GSM4462293 cell/sample type: cell lysate time point: 48h
## GSM4462294 cell/sample type: cell lysate time point: 48h
## characteristics_ch1.3
## GSM4462240 treatment/method: Untreated
## GSM4462241 treatment/method: Untreated
## GSM4462242 treatment/method: Untreated
## GSM4462243 treatment/method: Untreated
## GSM4462244 treatment/method: lipid nanoparticle (LNP)
## GSM4462245 treatment/method: lipid nanoparticle (LNP)
## GSM4462246 treatment/method: lipid nanoparticle (LNP)
## GSM4462247 treatment/method: lipid nanoparticle (LNP)
## GSM4462248 treatment/method: adeno-associated virus (AAV)
## GSM4462249 treatment/method: adeno-associated virus (AAV)
## GSM4462250 treatment/method: adeno-associated virus (AAV)
## GSM4462251 treatment/method: adeno-associated virus (AAV)
## GSM4462252 treatment/method: adeno-associated virus (AAV)
## GSM4462253 treatment/method: adeno-associated virus (AAV)
## GSM4462254 treatment/method: adeno-associated virus (AAV)
## GSM4462255 treatment/method: lipid nanoparticle (LNP)
## GSM4462256 treatment/method: lipid nanoparticle (LNP)
## GSM4462257 treatment/method: lipid nanoparticle (LNP)
## GSM4462258 treatment/method: lipid nanoparticle (LNP)
## GSM4462259 treatment/method: adeno-associated virus (AAV)
## GSM4462260 treatment/method: adeno-associated virus (AAV)
## GSM4462261 treatment/method: adeno-associated virus (AAV)
## GSM4462277 treatment/method: mRNA transfection
## GSM4462278 treatment/method: mRNA transfection
## GSM4462279 treatment/method: mRNA transfection
## GSM4462280 treatment/method: mRNA transfection
## GSM4462281 treatment/method: mRNA transfection
## GSM4462282 treatment/method: mRNA transfection
## GSM4462283 treatment/method: mRNA transfection
## GSM4462284 treatment/method: mRNA transfection
## GSM4462285 treatment/method: mRNA transfection
## GSM4462286 treatment/method: mRNA transfection
## GSM4462287 treatment/method: mRNA transfection
## GSM4462288 treatment/method: mRNA transfection
## GSM4462289 treatment/method: mRNA transfection
## GSM4462290 treatment/method: mRNA transfection
## GSM4462291 treatment/method: mRNA transfection
## GSM4462292 treatment/method: mRNA transfection
## GSM4462293 treatment/method: mRNA transfection
## GSM4462294 treatment/method: mRNA transfection
## characteristics_ch1.4 molecule_ch1
## GSM4462240 genotype/variation: none total RNA
## GSM4462241 genotype/variation: none total RNA
## GSM4462242 genotype/variation: none total RNA
## GSM4462243 genotype/variation: none total RNA
## GSM4462244 genotype/variation: saKKH-CBE3 total RNA
## GSM4462245 genotype/variation: saKKH-CBE3 total RNA
## GSM4462246 genotype/variation: saKKH-CBE3 total RNA
## GSM4462247 genotype/variation: saKKH-CBE3 total RNA
## GSM4462248 genotype/variation: saKKH-CBE3 total RNA
## GSM4462249 genotype/variation: saKKH-CBE3 total RNA
## GSM4462250 genotype/variation: saKKH-CBE3 total RNA
## GSM4462251 genotype/variation: saKKH-CBE3 total RNA
## GSM4462252 genotype/variation: saKKH-CBE3 total RNA
## GSM4462253 genotype/variation: saKKH-CBE3 total RNA
## GSM4462254 genotype/variation: saKKH-CBE3 total RNA
## GSM4462255 genotype/variation: saKKH-CBE3 total RNA
## GSM4462256 genotype/variation: saKKH-CBE3 total RNA
## GSM4462257 genotype/variation: saKKH-CBE3 total RNA
## GSM4462258 genotype/variation: saKKH-CBE3 total RNA
## GSM4462259 genotype/variation: saKKH-CBE3 total RNA
## GSM4462260 genotype/variation: saKKH-CBE3 total RNA
## GSM4462261 genotype/variation: saKKH-CBE3 total RNA
## GSM4462277 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462278 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462279 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462280 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462281 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462282 genotype/variation: RFP total RNA
## GSM4462283 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462284 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462285 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462286 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462287 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462288 genotype/variation: RFP total RNA
## GSM4462289 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462290 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462291 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462292 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462293 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462294 genotype/variation: RFP total RNA
## extract_protocol_ch1 taxid_ch1 description description.1
## GSM4462240 TruSeq RNA stranded 10090 20190725.B-1 20191015.B-1
## GSM4462241 TruSeq RNA stranded 10090 20190725.B-2 20191015.B-2
## GSM4462242 TruSeq RNA stranded 10090 20190725.B-3 20191015.B-3
## GSM4462243 TruSeq RNA stranded 10090 20190725.B-4 20191015.B-4
## GSM4462244 TruSeq RNA stranded 10090 20190725.B-5 20191015.B-5
## GSM4462245 TruSeq RNA stranded 10090 20190725.B-6 20191015.B-6
## GSM4462246 TruSeq RNA stranded 10090 20190725.B-7 20191015.B-7
## GSM4462247 TruSeq RNA stranded 10090 20190725.B-8 20191015.B-8
## GSM4462248 TruSeq RNA stranded 10090 20190725.B-9 20191015.B-9
## GSM4462249 TruSeq RNA stranded 10090 20190725.B-10 20191015.B-10
## GSM4462250 TruSeq RNA stranded 10090 20190725.B-11 20191015.B-11
## GSM4462251 TruSeq RNA stranded 10090 20190725.B-12 20191015.B-12
## GSM4462252 TruSeq RNA stranded 10090 20190725.B-13 20191015.B-13
## GSM4462253 TruSeq RNA stranded 10090 20190725.B-14 20191015.B-14
## GSM4462254 TruSeq RNA stranded 10090 20190725.B-15 20191015.B-15
## GSM4462255 TruSeq RNA stranded 10090 20190725.B-16 20191015.B-16
## GSM4462256 TruSeq RNA stranded 10090 20190725.B-17 20191015.B-17
## GSM4462257 TruSeq RNA stranded 10090 20190725.B-18 20191015.B-18
## GSM4462258 TruSeq RNA stranded 10090 20190725.B-19 20191015.B-19
## GSM4462259 TruSeq RNA stranded 10090 20190725.B-20 20191015.B-20
## GSM4462260 TruSeq RNA stranded 10090 20190725.B-21 20191015.B-21
## GSM4462261 TruSeq RNA stranded 10090 20190725.B-22 20191015.B-22
## GSM4462277 TruSeq RNA stranded 10090 20200320.A-4_rep1
## GSM4462278 TruSeq RNA stranded 10090 20200320.A-2_rep1
## GSM4462279 TruSeq RNA stranded 10090 20200320.A-1_rep1
## GSM4462280 TruSeq RNA stranded 10090 20200320.A-0_5_rep1
## GSM4462281 TruSeq RNA stranded 10090 20200320.A-0_25_rep1
## GSM4462282 TruSeq RNA stranded 10090 20200320.A-0_rep1
## GSM4462283 TruSeq RNA stranded 10090 20200320.A-4_rep2
## GSM4462284 TruSeq RNA stranded 10090 20200320.A-2_rep2
## GSM4462285 TruSeq RNA stranded 10090 20200320.A-1_rep2
## GSM4462286 TruSeq RNA stranded 10090 20200320.A-0_5_rep2
## GSM4462287 TruSeq RNA stranded 10090 20200320.A-0_25_rep2
## GSM4462288 TruSeq RNA stranded 10090 20200320.A-0_rep2
## GSM4462289 TruSeq RNA stranded 10090 20200320.A-4_rep3
## GSM4462290 TruSeq RNA stranded 10090 20200320.A-2_rep3
## GSM4462291 TruSeq RNA stranded 10090 20200320.A-1_rep3
## GSM4462292 TruSeq RNA stranded 10090 20200320.A-0_5_rep3
## GSM4462293 TruSeq RNA stranded 10090 20200320.A-0_25_rep3
## GSM4462294 TruSeq RNA stranded 10090 20200320.A-0_rep3
## data_processing
## GSM4462240 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462241 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462242 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462243 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462244 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462245 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462246 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462247 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462248 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462249 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462250 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462251 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462252 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462253 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462254 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462255 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462256 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462257 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462258 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462259 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462260 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462261 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462277 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462278 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462279 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462280 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462281 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462282 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462283 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462284 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462285 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462286 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462287 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462288 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462289 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462290 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462291 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462292 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462293 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462294 Raw reads were trimmed and filtered using fastp version version 0.20.0
## data_processing.1
## GSM4462240 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462241 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462242 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462243 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462244 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462245 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462246 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462247 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462248 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462249 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462250 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462251 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462252 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462253 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462254 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462255 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462256 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462257 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462258 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462259 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462260 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462261 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462277 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462278 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462279 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462280 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462281 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462282 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462283 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462284 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462285 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462286 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462287 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462288 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462289 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462290 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462291 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462292 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462293 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462294 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## data_processing.2
## GSM4462240 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462241 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462242 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462243 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462244 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462245 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462246 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462247 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462248 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462249 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462250 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462251 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462252 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462253 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462254 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462255 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462256 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462257 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462258 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462259 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462260 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462261 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462277 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462278 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462279 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462280 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462281 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462282 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462283 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462284 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462285 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462286 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462287 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462288 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462289 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462290 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462291 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462292 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462293 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462294 Trancript level normalized counts were generated using kllisto version 0.44.0
## data_processing.3
## GSM4462240 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462241 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462242 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462243 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462244 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462245 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462246 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462247 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462248 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462249 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462250 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462251 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462252 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462253 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462254 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462255 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462256 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462257 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462258 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462259 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462260 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462261 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462277 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462278 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462279 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462280 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462281 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462282 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462283 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462284 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462285 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462286 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462287 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462288 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462289 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462290 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462291 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462292 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462293 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462294 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## data_processing.4
## GSM4462240 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462241 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462242 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462243 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462244 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462245 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462246 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462247 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462248 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462249 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462250 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462251 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462252 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462253 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462254 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462255 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462256 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462257 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462258 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462259 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462260 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462261 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462277 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462278 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462279 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462280 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462281 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462282 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462283 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462284 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462285 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462286 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462287 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462288 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462289 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462290 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462291 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462292 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462293 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462294 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## platform_id contact_name contact_email contact_department
## GSM4462240 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462241 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462242 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462243 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462244 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462245 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462246 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462247 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462248 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462249 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462250 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462251 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462252 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462253 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462254 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462255 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462256 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462257 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462258 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462259 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462260 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462261 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462277 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462278 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462279 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462280 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462281 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462282 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462283 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462284 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462285 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462286 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462287 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462288 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462289 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462290 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462291 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462292 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462293 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462294 GPL24247 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## contact_institute contact_address contact_city
## GSM4462240 ETHZ Winterthurerstr. 190 Zurich
## GSM4462241 ETHZ Winterthurerstr. 190 Zurich
## GSM4462242 ETHZ Winterthurerstr. 190 Zurich
## GSM4462243 ETHZ Winterthurerstr. 190 Zurich
## GSM4462244 ETHZ Winterthurerstr. 190 Zurich
## GSM4462245 ETHZ Winterthurerstr. 190 Zurich
## GSM4462246 ETHZ Winterthurerstr. 190 Zurich
## GSM4462247 ETHZ Winterthurerstr. 190 Zurich
## GSM4462248 ETHZ Winterthurerstr. 190 Zurich
## GSM4462249 ETHZ Winterthurerstr. 190 Zurich
## GSM4462250 ETHZ Winterthurerstr. 190 Zurich
## GSM4462251 ETHZ Winterthurerstr. 190 Zurich
## GSM4462252 ETHZ Winterthurerstr. 190 Zurich
## GSM4462253 ETHZ Winterthurerstr. 190 Zurich
## GSM4462254 ETHZ Winterthurerstr. 190 Zurich
## GSM4462255 ETHZ Winterthurerstr. 190 Zurich
## GSM4462256 ETHZ Winterthurerstr. 190 Zurich
## GSM4462257 ETHZ Winterthurerstr. 190 Zurich
## GSM4462258 ETHZ Winterthurerstr. 190 Zurich
## GSM4462259 ETHZ Winterthurerstr. 190 Zurich
## GSM4462260 ETHZ Winterthurerstr. 190 Zurich
## GSM4462261 ETHZ Winterthurerstr. 190 Zurich
## GSM4462277 ETHZ Winterthurerstr. 190 Zurich
## GSM4462278 ETHZ Winterthurerstr. 190 Zurich
## GSM4462279 ETHZ Winterthurerstr. 190 Zurich
## GSM4462280 ETHZ Winterthurerstr. 190 Zurich
## GSM4462281 ETHZ Winterthurerstr. 190 Zurich
## GSM4462282 ETHZ Winterthurerstr. 190 Zurich
## GSM4462283 ETHZ Winterthurerstr. 190 Zurich
## GSM4462284 ETHZ Winterthurerstr. 190 Zurich
## GSM4462285 ETHZ Winterthurerstr. 190 Zurich
## GSM4462286 ETHZ Winterthurerstr. 190 Zurich
## GSM4462287 ETHZ Winterthurerstr. 190 Zurich
## GSM4462288 ETHZ Winterthurerstr. 190 Zurich
## GSM4462289 ETHZ Winterthurerstr. 190 Zurich
## GSM4462290 ETHZ Winterthurerstr. 190 Zurich
## GSM4462291 ETHZ Winterthurerstr. 190 Zurich
## GSM4462292 ETHZ Winterthurerstr. 190 Zurich
## GSM4462293 ETHZ Winterthurerstr. 190 Zurich
## GSM4462294 ETHZ Winterthurerstr. 190 Zurich
## contact_zip/postal_code contact_country data_row_count
## GSM4462240 8075 Switzerland 0
## GSM4462241 8075 Switzerland 0
## GSM4462242 8075 Switzerland 0
## GSM4462243 8075 Switzerland 0
## GSM4462244 8075 Switzerland 0
## GSM4462245 8075 Switzerland 0
## GSM4462246 8075 Switzerland 0
## GSM4462247 8075 Switzerland 0
## GSM4462248 8075 Switzerland 0
## GSM4462249 8075 Switzerland 0
## GSM4462250 8075 Switzerland 0
## GSM4462251 8075 Switzerland 0
## GSM4462252 8075 Switzerland 0
## GSM4462253 8075 Switzerland 0
## GSM4462254 8075 Switzerland 0
## GSM4462255 8075 Switzerland 0
## GSM4462256 8075 Switzerland 0
## GSM4462257 8075 Switzerland 0
## GSM4462258 8075 Switzerland 0
## GSM4462259 8075 Switzerland 0
## GSM4462260 8075 Switzerland 0
## GSM4462261 8075 Switzerland 0
## GSM4462277 8075 Switzerland 0
## GSM4462278 8075 Switzerland 0
## GSM4462279 8075 Switzerland 0
## GSM4462280 8075 Switzerland 0
## GSM4462281 8075 Switzerland 0
## GSM4462282 8075 Switzerland 0
## GSM4462283 8075 Switzerland 0
## GSM4462284 8075 Switzerland 0
## GSM4462285 8075 Switzerland 0
## GSM4462286 8075 Switzerland 0
## GSM4462287 8075 Switzerland 0
## GSM4462288 8075 Switzerland 0
## GSM4462289 8075 Switzerland 0
## GSM4462290 8075 Switzerland 0
## GSM4462291 8075 Switzerland 0
## GSM4462292 8075 Switzerland 0
## GSM4462293 8075 Switzerland 0
## GSM4462294 8075 Switzerland 0
## instrument_model library_selection library_source
## GSM4462240 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462241 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462242 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462243 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462244 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462245 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462246 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462247 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462248 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462249 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462250 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462251 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462252 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462253 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462254 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462255 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462256 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462257 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462258 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462259 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462260 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462261 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462277 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462278 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462279 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462280 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462281 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462282 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462283 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462284 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462285 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462286 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462287 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462288 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462289 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462290 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462291 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462292 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462293 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462294 Illumina NovaSeq 6000 cDNA transcriptomic
## library_strategy
## GSM4462240 RNA-Seq
## GSM4462241 RNA-Seq
## GSM4462242 RNA-Seq
## GSM4462243 RNA-Seq
## GSM4462244 RNA-Seq
## GSM4462245 RNA-Seq
## GSM4462246 RNA-Seq
## GSM4462247 RNA-Seq
## GSM4462248 RNA-Seq
## GSM4462249 RNA-Seq
## GSM4462250 RNA-Seq
## GSM4462251 RNA-Seq
## GSM4462252 RNA-Seq
## GSM4462253 RNA-Seq
## GSM4462254 RNA-Seq
## GSM4462255 RNA-Seq
## GSM4462256 RNA-Seq
## GSM4462257 RNA-Seq
## GSM4462258 RNA-Seq
## GSM4462259 RNA-Seq
## GSM4462260 RNA-Seq
## GSM4462261 RNA-Seq
## GSM4462277 RNA-Seq
## GSM4462278 RNA-Seq
## GSM4462279 RNA-Seq
## GSM4462280 RNA-Seq
## GSM4462281 RNA-Seq
## GSM4462282 RNA-Seq
## GSM4462283 RNA-Seq
## GSM4462284 RNA-Seq
## GSM4462285 RNA-Seq
## GSM4462286 RNA-Seq
## GSM4462287 RNA-Seq
## GSM4462288 RNA-Seq
## GSM4462289 RNA-Seq
## GSM4462290 RNA-Seq
## GSM4462291 RNA-Seq
## GSM4462292 RNA-Seq
## GSM4462293 RNA-Seq
## GSM4462294 RNA-Seq
## relation
## GSM4462240 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563107
## GSM4462241 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563106
## GSM4462242 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563105
## GSM4462243 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563104
## GSM4462244 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563103
## GSM4462245 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563102
## GSM4462246 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563101
## GSM4462247 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563100
## GSM4462248 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563099
## GSM4462249 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563098
## GSM4462250 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563097
## GSM4462251 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563096
## GSM4462252 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563095
## GSM4462253 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563094
## GSM4462254 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563093
## GSM4462255 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563092
## GSM4462256 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563091
## GSM4462257 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563090
## GSM4462258 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563089
## GSM4462259 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563088
## GSM4462260 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563087
## GSM4462261 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563086
## GSM4462277 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563110
## GSM4462278 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563109
## GSM4462279 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563108
## GSM4462280 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563150
## GSM4462281 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563149
## GSM4462282 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563148
## GSM4462283 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563147
## GSM4462284 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563146
## GSM4462285 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563145
## GSM4462286 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563144
## GSM4462287 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563143
## GSM4462288 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563142
## GSM4462289 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563141
## GSM4462290 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563140
## GSM4462291 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563139
## GSM4462292 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563138
## GSM4462293 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563137
## GSM4462294 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563136
## relation.1
## GSM4462240 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086038
## GSM4462241 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086039
## GSM4462242 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086040
## GSM4462243 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086041
## GSM4462244 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086042
## GSM4462245 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086043
## GSM4462246 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086044
## GSM4462247 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086045
## GSM4462248 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086046
## GSM4462249 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086047
## GSM4462250 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086048
## GSM4462251 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086049
## GSM4462252 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086050
## GSM4462253 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086051
## GSM4462254 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086052
## GSM4462255 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086053
## GSM4462256 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086054
## GSM4462257 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086055
## GSM4462258 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086056
## GSM4462259 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086057
## GSM4462260 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086058
## GSM4462261 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086059
## GSM4462277 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086075
## GSM4462278 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086076
## GSM4462279 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086077
## GSM4462280 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086078
## GSM4462281 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086079
## GSM4462282 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086080
## GSM4462283 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086081
## GSM4462284 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086082
## GSM4462285 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086083
## GSM4462286 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086084
## GSM4462287 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086085
## GSM4462288 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086086
## GSM4462289 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086087
## GSM4462290 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086088
## GSM4462291 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086089
## GSM4462292 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086090
## GSM4462293 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086091
## GSM4462294 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086092
## supplementary_file_1
## GSM4462240 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462240/suppl/GSM4462240_1_abundance.tsv.gz
## GSM4462241 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462241/suppl/GSM4462241_2_abundance.tsv.gz
## GSM4462242 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462242/suppl/GSM4462242_3_abundance.tsv.gz
## GSM4462243 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462243/suppl/GSM4462243_4_abundance.tsv.gz
## GSM4462244 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462244/suppl/GSM4462244_5_abundance.tsv.gz
## GSM4462245 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462245/suppl/GSM4462245_6_abundance.tsv.gz
## GSM4462246 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462246/suppl/GSM4462246_7_abundance.tsv.gz
## GSM4462247 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462247/suppl/GSM4462247_8_abundance.tsv.gz
## GSM4462248 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462248/suppl/GSM4462248_9_abundance.tsv.gz
## GSM4462249 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462249/suppl/GSM4462249_10_abundance.tsv.gz
## GSM4462250 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462250/suppl/GSM4462250_11_abundance.tsv.gz
## GSM4462251 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462251/suppl/GSM4462251_12_abundance.tsv.gz
## GSM4462252 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462252/suppl/GSM4462252_13_abundance.tsv.gz
## GSM4462253 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462253/suppl/GSM4462253_14_abundance.tsv.gz
## GSM4462254 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462254/suppl/GSM4462254_15_abundance.tsv.gz
## GSM4462255 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462255/suppl/GSM4462255_16_abundance.tsv.gz
## GSM4462256 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462256/suppl/GSM4462256_17_abundance.tsv.gz
## GSM4462257 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462257/suppl/GSM4462257_18_abundance.tsv.gz
## GSM4462258 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462258/suppl/GSM4462258_19_abundance.tsv.gz
## GSM4462259 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462259/suppl/GSM4462259_20_abundance.tsv.gz
## GSM4462260 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462260/suppl/GSM4462260_21_abundance.tsv.gz
## GSM4462261 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462261/suppl/GSM4462261_22_abundance.tsv.gz
## GSM4462277 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462277/suppl/GSM4462277_20200320.A-4_rep1_abundance.tsv.gz
## GSM4462278 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462278/suppl/GSM4462278_20200320.A-2_rep1_abundance.tsv.gz
## GSM4462279 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462279/suppl/GSM4462279_20200320.A-1_rep1_abundance.tsv.gz
## GSM4462280 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462280/suppl/GSM4462280_20200320.A-0_5_rep1_abundance.tsv.gz
## GSM4462281 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462281/suppl/GSM4462281_20200320.A-0_25_rep1_abundance.tsv.gz
## GSM4462282 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462282/suppl/GSM4462282_20200320.A-0_rep1_abundance.tsv.gz
## GSM4462283 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462283/suppl/GSM4462283_20200320.A-4_rep2_abundance.tsv.gz
## GSM4462284 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462284/suppl/GSM4462284_20200320.A-2_rep2_abundance.tsv.gz
## GSM4462285 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462285/suppl/GSM4462285_20200320.A-1_rep2_abundance.tsv.gz
## GSM4462286 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462286/suppl/GSM4462286_20200320.A-0_5_rep2_abundance.tsv.gz
## GSM4462287 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462287/suppl/GSM4462287_20200320.A-0_25_rep2_abundance.tsv.gz
## GSM4462288 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462288/suppl/GSM4462288_20200320.A-0_rep2_abundance.tsv.gz
## GSM4462289 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462289/suppl/GSM4462289_20200320.A-4_rep3_abundance.tsv.gz
## GSM4462290 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462290/suppl/GSM4462290_20200320.A-2_rep3_abundance.tsv.gz
## GSM4462291 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462291/suppl/GSM4462291_20200320.A-1_rep3_abundance.tsv.gz
## GSM4462292 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462292/suppl/GSM4462292_20200320.A-0_5_rep3_abundance.tsv.gz
## GSM4462293 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462293/suppl/GSM4462293_20200320.A-0_25_rep3_abundance.tsv.gz
## GSM4462294 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462294/suppl/GSM4462294_20200320.A-0_rep3_abundance.tsv.gz
## cell line/strain:ch1 cell/sample type:ch1 genotype/variation:ch1
## GSM4462240 Pah-enu2 Liver none
## GSM4462241 Pah-enu2 Liver none
## GSM4462242 Pah-enu2 Liver none
## GSM4462243 Pah-enu2 Liver none
## GSM4462244 Pah-enu2 Liver saKKH-CBE3
## GSM4462245 Pah-enu2 Liver saKKH-CBE3
## GSM4462246 Pah-enu2 Liver saKKH-CBE3
## GSM4462247 Pah-enu2 Liver saKKH-CBE3
## GSM4462248 Pah-enu2 Liver saKKH-CBE3
## GSM4462249 Pah-enu2 Liver saKKH-CBE3
## GSM4462250 Pah-enu2 Liver saKKH-CBE3
## GSM4462251 Pah-enu2 Liver saKKH-CBE3
## GSM4462252 Pah-enu2 Liver saKKH-CBE3
## GSM4462253 Pah-enu2 Liver saKKH-CBE3
## GSM4462254 Pah-enu2 Liver saKKH-CBE3
## GSM4462255 Pah-enu2 Liver saKKH-CBE3
## GSM4462256 Pah-enu2 Liver saKKH-CBE3
## GSM4462257 Pah-enu2 Liver saKKH-CBE3
## GSM4462258 Pah-enu2 Liver saKKH-CBE3
## GSM4462259 Pah-enu2 Liver saKKH-CBE3
## GSM4462260 Pah-enu2 Liver saKKH-CBE3
## GSM4462261 Pah-enu2 Liver saKKH-CBE3
## GSM4462277 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462278 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462279 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462280 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462281 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462282 Hepa1-6 cell lysate RFP
## GSM4462283 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462284 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462285 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462286 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462287 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462288 Hepa1-6 cell lysate RFP
## GSM4462289 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462290 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462291 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462292 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462293 Hepa1-6 cell lysate saKKH-CBE3 + RFP
## GSM4462294 Hepa1-6 cell lysate RFP
## time point:ch1 treatment/method:ch1
## GSM4462240 0 Untreated
## GSM4462241 0 Untreated
## GSM4462242 0 Untreated
## GSM4462243 0 Untreated
## GSM4462244 1m lipid nanoparticle (LNP)
## GSM4462245 1m lipid nanoparticle (LNP)
## GSM4462246 1m lipid nanoparticle (LNP)
## GSM4462247 1m lipid nanoparticle (LNP)
## GSM4462248 16m adeno-associated virus (AAV)
## GSM4462249 16m adeno-associated virus (AAV)
## GSM4462250 16m adeno-associated virus (AAV)
## GSM4462251 16m adeno-associated virus (AAV)
## GSM4462252 16m adeno-associated virus (AAV)
## GSM4462253 16m adeno-associated virus (AAV)
## GSM4462254 16m adeno-associated virus (AAV)
## GSM4462255 48h lipid nanoparticle (LNP)
## GSM4462256 48h lipid nanoparticle (LNP)
## GSM4462257 48h lipid nanoparticle (LNP)
## GSM4462258 48h lipid nanoparticle (LNP)
## GSM4462259 2m adeno-associated virus (AAV)
## GSM4462260 2m adeno-associated virus (AAV)
## GSM4462261 2m adeno-associated virus (AAV)
## GSM4462277 48h mRNA transfection
## GSM4462278 48h mRNA transfection
## GSM4462279 48h mRNA transfection
## GSM4462280 48h mRNA transfection
## GSM4462281 48h mRNA transfection
## GSM4462282 48h mRNA transfection
## GSM4462283 48h mRNA transfection
## GSM4462284 48h mRNA transfection
## GSM4462285 48h mRNA transfection
## GSM4462286 48h mRNA transfection
## GSM4462287 48h mRNA transfection
## GSM4462288 48h mRNA transfection
## GSM4462289 48h mRNA transfection
## GSM4462290 48h mRNA transfection
## GSM4462291 48h mRNA transfection
## GSM4462292 48h mRNA transfection
## GSM4462293 48h mRNA transfection
## GSM4462294 48h mRNA transfection
##
## $`GSE148349-GPL24676`
## title geo_accession
## GSM4462262 Full intein, top 5% RFP [p3138_6230/1] GSM4462262
## GSM4462263 Full intein, top 5% RFP [p3138_6230/2] GSM4462263
## GSM4462264 Full intein, top 5% RFP [p3138_6230/3] GSM4462264
## GSM4462265 RFP control [p3138_6230/4] GSM4462265
## GSM4462266 RFP control [p3138_6230/5] GSM4462266
## GSM4462267 RFP control [p3138_6230/6] GSM4462267
## GSM4462268 BE3-spCas, top 5% GFP [p3138_6230/7] GSM4462268
## GSM4462269 BE3-spCas, top 5% GFP [p3138_6230/8] GSM4462269
## GSM4462270 BE3-spCas, top 5% GFP [p3138_6230/9] GSM4462270
## GSM4462271 BE3-saCas, top 5% GFP [p3138_6230/10] GSM4462271
## GSM4462272 BE3-saCas, top 5% GFP [p3138_6230/11] GSM4462272
## GSM4462273 BE3-saCas, top 5% GFP [p3138_6230/12] GSM4462273
## GSM4462274 GFP control [p3138_6230/13] GSM4462274
## GSM4462275 GFP control [p3138_6230/14] GSM4462275
## GSM4462276 GFP control [p3138_6230/15] GSM4462276
## GSM4462295 HEK_1high_rep1 [p3138_o6813/1] GSM4462295
## GSM4462296 HEK_2_rep1 [p3138_o6813/2] GSM4462296
## GSM4462297 HEK_3_rep1 [p3138_o6813/3] GSM4462297
## GSM4462298 HEK_4_rep1 [p3138_o6813/4] GSM4462298
## GSM4462299 HEK_1high_rep2 [p3138_o6813/5] GSM4462299
## GSM4462300 HEK_2_rep2 [p3138_o6813/6] GSM4462300
## GSM4462301 HEK_3_rep2 [p3138_o6813/7] GSM4462301
## GSM4462302 HEK_4_rep2 [p3138_o6813/8] GSM4462302
## GSM4462303 HEK_1high_rep3 [p3138_o6813/9] GSM4462303
## GSM4462304 HEK_2_rep3 [p3138_o6813/10] GSM4462304
## GSM4462305 HEK_3_rep3 [p3138_o6813/11] GSM4462305
## status submission_date last_update_date type
## GSM4462262 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462263 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462264 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462265 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462266 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462267 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462268 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462269 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462270 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462271 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462272 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462273 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462274 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462275 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462276 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462295 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462296 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462297 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462298 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462299 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462300 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462301 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462302 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462303 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462304 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## GSM4462305 Public on Aug 24 2020 Apr 08 2020 Aug 25 2020 SRA
## channel_count source_name_ch1 organism_ch1
## GSM4462262 1 HEK293T_Full intein, top 5% RFP Homo sapiens
## GSM4462263 1 HEK293T_Full intein, top 5% RFP Homo sapiens
## GSM4462264 1 HEK293T_Full intein, top 5% RFP Homo sapiens
## GSM4462265 1 HEK293T_RFP control Homo sapiens
## GSM4462266 1 HEK293T_RFP control Homo sapiens
## GSM4462267 1 HEK293T_RFP control Homo sapiens
## GSM4462268 1 HEK293T_BE3-spCas, top 5% GFP Homo sapiens
## GSM4462269 1 HEK293T_BE3-spCas, top 5% GFP Homo sapiens
## GSM4462270 1 HEK293T_BE3-spCas, top 5% GFP Homo sapiens
## GSM4462271 1 HEK293T_BE3-saCas, top 5% GFP Homo sapiens
## GSM4462272 1 HEK293T_BE3-saCas, top 5% GFP Homo sapiens
## GSM4462273 1 HEK293T_BE3-saCas, top 5% GFP Homo sapiens
## GSM4462274 1 HEK293T_GFP control Homo sapiens
## GSM4462275 1 HEK293T_GFP control Homo sapiens
## GSM4462276 1 HEK293T_GFP control Homo sapiens
## GSM4462295 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462296 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462297 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462298 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462299 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462300 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462301 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462302 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462303 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462304 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## GSM4462305 1 HEK293T_saKKH-CBE3 + RFP_48h Homo sapiens
## characteristics_ch1 characteristics_ch1.1
## GSM4462262 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462263 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462264 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462265 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462266 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462267 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462268 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462269 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462270 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462271 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462272 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462273 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462274 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462275 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462276 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462295 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462296 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462297 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462298 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462299 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462300 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462301 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462302 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462303 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462304 cell line/strain: HEK293T cell/sample type: cell lysate
## GSM4462305 cell line/strain: HEK293T cell/sample type: cell lysate
## characteristics_ch1.2 characteristics_ch1.3
## GSM4462262 time point: 72h treatment/method: Plasmid transfection
## GSM4462263 time point: 72h treatment/method: Plasmid transfection
## GSM4462264 time point: 72h treatment/method: Plasmid transfection
## GSM4462265 time point: 0 treatment/method: Plasmid transfection
## GSM4462266 time point: 0 treatment/method: Plasmid transfection
## GSM4462267 time point: 0 treatment/method: Plasmid transfection
## GSM4462268 time point: 72h treatment/method: Plasmid transfection
## GSM4462269 time point: 72h treatment/method: Plasmid transfection
## GSM4462270 time point: 72h treatment/method: Plasmid transfection
## GSM4462271 time point: 72h treatment/method: Plasmid transfection
## GSM4462272 time point: 72h treatment/method: Plasmid transfection
## GSM4462273 time point: 72h treatment/method: Plasmid transfection
## GSM4462274 time point: 0 treatment/method: Plasmid transfection
## GSM4462275 time point: 0 treatment/method: Plasmid transfection
## GSM4462276 time point: 0 treatment/method: Plasmid transfection
## GSM4462295 time point: 48h treatment/method: mRNA transfection
## GSM4462296 time point: 48h treatment/method: mRNA transfection
## GSM4462297 time point: 48h treatment/method: mRNA transfection
## GSM4462298 time point: 48h treatment/method: mRNA transfection
## GSM4462299 time point: 48h treatment/method: mRNA transfection
## GSM4462300 time point: 48h treatment/method: mRNA transfection
## GSM4462301 time point: 48h treatment/method: mRNA transfection
## GSM4462302 time point: 48h treatment/method: mRNA transfection
## GSM4462303 time point: 48h treatment/method: mRNA transfection
## GSM4462304 time point: 48h treatment/method: mRNA transfection
## GSM4462305 time point: 48h treatment/method: mRNA transfection
## characteristics_ch1.4 molecule_ch1
## GSM4462262 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462263 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462264 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462265 genotype/variation: RFP total RNA
## GSM4462266 genotype/variation: RFP total RNA
## GSM4462267 genotype/variation: RFP total RNA
## GSM4462268 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462269 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462270 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462271 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462272 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462273 genotype/variation: saKKH-CBE3 + GFP total RNA
## GSM4462274 genotype/variation: GFP total RNA
## GSM4462275 genotype/variation: GFP total RNA
## GSM4462276 genotype/variation: GFP total RNA
## GSM4462295 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462296 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462297 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462298 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462299 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462300 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462301 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462302 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462303 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462304 genotype/variation: saKKH-CBE3 + RFP total RNA
## GSM4462305 genotype/variation: saKKH-CBE3 + RFP total RNA
## extract_protocol_ch1 taxid_ch1
## GSM4462262 TruSeq RNA stranded 9606
## GSM4462263 TruSeq RNA stranded 9606
## GSM4462264 TruSeq RNA stranded 9606
## GSM4462265 TruSeq RNA stranded 9606
## GSM4462266 TruSeq RNA stranded 9606
## GSM4462267 TruSeq RNA stranded 9606
## GSM4462268 TruSeq RNA stranded 9606
## GSM4462269 TruSeq RNA stranded 9606
## GSM4462270 TruSeq RNA stranded 9606
## GSM4462271 TruSeq RNA stranded 9606
## GSM4462272 TruSeq RNA stranded 9606
## GSM4462273 TruSeq RNA stranded 9606
## GSM4462274 TruSeq RNA stranded 9606
## GSM4462275 TruSeq RNA stranded 9606
## GSM4462276 TruSeq RNA stranded 9606
## GSM4462295 TruSeq RNA stranded 9606
## GSM4462296 TruSeq RNA stranded 9606
## GSM4462297 TruSeq RNA stranded 9606
## GSM4462298 TruSeq RNA stranded 9606
## GSM4462299 TruSeq RNA stranded 9606
## GSM4462300 TruSeq RNA stranded 9606
## GSM4462301 TruSeq RNA stranded 9606
## GSM4462302 TruSeq RNA stranded 9606
## GSM4462303 TruSeq RNA stranded 9606
## GSM4462304 TruSeq RNA stranded 9606
## GSM4462305 TruSeq RNA stranded 9606
## description
## GSM4462262 20191029.A-full_intein_uppest5_RFP_1
## GSM4462263 20191029.A-full_intein_uppest5_RFP_2
## GSM4462264 20191029.A-full_intein_uppest5_RFP_3
## GSM4462265 20191029.A-c-intein_RFP_control_uppest5_RFP_1
## GSM4462266 20191029.A-c-intein_RFP_control_uppest5_RFP_2
## GSM4462267 20191029.A-c-intein_RFP_control_uppest5_RFP_3
## GSM4462268 20191029.A-GFP_spCas_uppest5_1
## GSM4462269 20191029.A-GFP_spCas_uppest5_2
## GSM4462270 20191029.A-GFP_spCas_uppest5_3
## GSM4462271 20191029.A-GFP_saCas_uppest5_1
## GSM4462272 20191029.A-GFP_saCas_uppest5_2
## GSM4462273 20191029.A-GFP_saCas_uppest5_3
## GSM4462274 20191029.A-GFP_ctrl_uppest5_1
## GSM4462275 20191029.A-GFP_ctrl_uppest5_2
## GSM4462276 20191029.A-GFP_ctrl_uppest5_3
## GSM4462295 20200320.A-HEK_1high_rep1
## GSM4462296 20200320.A-HEK_2_rep1
## GSM4462297 20200320.A-HEK_3_rep1
## GSM4462298 20200320.A-HEK_4_rep1
## GSM4462299 20200320.A-HEK_1high_rep2
## GSM4462300 20200320.A-HEK_2_rep2
## GSM4462301 20200320.A-HEK_3_rep2
## GSM4462302 20200320.A-HEK_4_rep2
## GSM4462303 20200320.A-HEK_1high_rep3
## GSM4462304 20200320.A-HEK_2_rep3
## GSM4462305 20200320.A-HEK_3_rep3
## data_processing
## GSM4462262 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462263 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462264 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462265 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462266 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462267 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462268 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462269 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462270 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462271 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462272 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462273 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462274 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462275 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462276 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462295 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462296 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462297 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462298 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462299 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462300 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462301 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462302 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462303 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462304 Raw reads were trimmed and filtered using fastp version version 0.20.0
## GSM4462305 Raw reads were trimmed and filtered using fastp version version 0.20.0
## data_processing.1
## GSM4462262 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462263 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462264 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462265 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462266 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462267 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462268 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462269 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462270 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462271 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462272 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462273 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462274 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462275 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462276 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462295 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462296 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462297 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462298 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462299 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462300 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462301 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462302 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462303 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462304 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## GSM4462305 Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
## data_processing.2
## GSM4462262 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462263 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462264 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462265 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462266 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462267 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462268 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462269 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462270 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462271 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462272 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462273 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462274 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462275 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462276 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462295 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462296 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462297 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462298 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462299 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462300 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462301 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462302 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462303 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462304 Trancript level normalized counts were generated using kllisto version 0.44.0
## GSM4462305 Trancript level normalized counts were generated using kllisto version 0.44.0
## data_processing.3
## GSM4462262 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462263 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462264 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462265 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462266 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462267 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462268 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462269 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462270 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462271 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462272 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462273 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462274 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462275 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462276 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462295 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462296 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462297 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462298 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462299 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462300 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462301 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462302 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462303 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462304 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## GSM4462305 Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
## data_processing.4
## GSM4462262 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462263 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462264 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462265 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462266 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462267 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462268 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462269 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462270 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462271 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462272 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462273 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462274 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462275 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462276 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462295 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462296 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462297 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462298 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462299 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462300 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462301 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462302 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462303 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462304 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## GSM4462305 Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)
## platform_id contact_name contact_email contact_department
## GSM4462262 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462263 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462264 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462265 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462266 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462267 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462268 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462269 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462270 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462271 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462272 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462273 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462274 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462275 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462276 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462295 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462296 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462297 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462298 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462299 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462300 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462301 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462302 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462303 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462304 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## GSM4462305 GPL24676 Weihong,,Qi weihong.qi@fgcz.ethz.ch FGCZ
## contact_institute contact_address contact_city
## GSM4462262 ETHZ Winterthurerstr. 190 Zurich
## GSM4462263 ETHZ Winterthurerstr. 190 Zurich
## GSM4462264 ETHZ Winterthurerstr. 190 Zurich
## GSM4462265 ETHZ Winterthurerstr. 190 Zurich
## GSM4462266 ETHZ Winterthurerstr. 190 Zurich
## GSM4462267 ETHZ Winterthurerstr. 190 Zurich
## GSM4462268 ETHZ Winterthurerstr. 190 Zurich
## GSM4462269 ETHZ Winterthurerstr. 190 Zurich
## GSM4462270 ETHZ Winterthurerstr. 190 Zurich
## GSM4462271 ETHZ Winterthurerstr. 190 Zurich
## GSM4462272 ETHZ Winterthurerstr. 190 Zurich
## GSM4462273 ETHZ Winterthurerstr. 190 Zurich
## GSM4462274 ETHZ Winterthurerstr. 190 Zurich
## GSM4462275 ETHZ Winterthurerstr. 190 Zurich
## GSM4462276 ETHZ Winterthurerstr. 190 Zurich
## GSM4462295 ETHZ Winterthurerstr. 190 Zurich
## GSM4462296 ETHZ Winterthurerstr. 190 Zurich
## GSM4462297 ETHZ Winterthurerstr. 190 Zurich
## GSM4462298 ETHZ Winterthurerstr. 190 Zurich
## GSM4462299 ETHZ Winterthurerstr. 190 Zurich
## GSM4462300 ETHZ Winterthurerstr. 190 Zurich
## GSM4462301 ETHZ Winterthurerstr. 190 Zurich
## GSM4462302 ETHZ Winterthurerstr. 190 Zurich
## GSM4462303 ETHZ Winterthurerstr. 190 Zurich
## GSM4462304 ETHZ Winterthurerstr. 190 Zurich
## GSM4462305 ETHZ Winterthurerstr. 190 Zurich
## contact_zip/postal_code contact_country data_row_count
## GSM4462262 8075 Switzerland 0
## GSM4462263 8075 Switzerland 0
## GSM4462264 8075 Switzerland 0
## GSM4462265 8075 Switzerland 0
## GSM4462266 8075 Switzerland 0
## GSM4462267 8075 Switzerland 0
## GSM4462268 8075 Switzerland 0
## GSM4462269 8075 Switzerland 0
## GSM4462270 8075 Switzerland 0
## GSM4462271 8075 Switzerland 0
## GSM4462272 8075 Switzerland 0
## GSM4462273 8075 Switzerland 0
## GSM4462274 8075 Switzerland 0
## GSM4462275 8075 Switzerland 0
## GSM4462276 8075 Switzerland 0
## GSM4462295 8075 Switzerland 0
## GSM4462296 8075 Switzerland 0
## GSM4462297 8075 Switzerland 0
## GSM4462298 8075 Switzerland 0
## GSM4462299 8075 Switzerland 0
## GSM4462300 8075 Switzerland 0
## GSM4462301 8075 Switzerland 0
## GSM4462302 8075 Switzerland 0
## GSM4462303 8075 Switzerland 0
## GSM4462304 8075 Switzerland 0
## GSM4462305 8075 Switzerland 0
## instrument_model library_selection library_source
## GSM4462262 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462263 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462264 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462265 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462266 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462267 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462268 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462269 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462270 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462271 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462272 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462273 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462274 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462275 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462276 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462295 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462296 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462297 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462298 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462299 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462300 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462301 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462302 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462303 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462304 Illumina NovaSeq 6000 cDNA transcriptomic
## GSM4462305 Illumina NovaSeq 6000 cDNA transcriptomic
## library_strategy
## GSM4462262 RNA-Seq
## GSM4462263 RNA-Seq
## GSM4462264 RNA-Seq
## GSM4462265 RNA-Seq
## GSM4462266 RNA-Seq
## GSM4462267 RNA-Seq
## GSM4462268 RNA-Seq
## GSM4462269 RNA-Seq
## GSM4462270 RNA-Seq
## GSM4462271 RNA-Seq
## GSM4462272 RNA-Seq
## GSM4462273 RNA-Seq
## GSM4462274 RNA-Seq
## GSM4462275 RNA-Seq
## GSM4462276 RNA-Seq
## GSM4462295 RNA-Seq
## GSM4462296 RNA-Seq
## GSM4462297 RNA-Seq
## GSM4462298 RNA-Seq
## GSM4462299 RNA-Seq
## GSM4462300 RNA-Seq
## GSM4462301 RNA-Seq
## GSM4462302 RNA-Seq
## GSM4462303 RNA-Seq
## GSM4462304 RNA-Seq
## GSM4462305 RNA-Seq
## relation
## GSM4462262 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563085
## GSM4462263 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563130
## GSM4462264 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563129
## GSM4462265 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563128
## GSM4462266 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563127
## GSM4462267 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563116
## GSM4462268 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563115
## GSM4462269 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563114
## GSM4462270 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563126
## GSM4462271 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563125
## GSM4462272 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563124
## GSM4462273 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563117
## GSM4462274 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563113
## GSM4462275 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563112
## GSM4462276 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563111
## GSM4462295 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563135
## GSM4462296 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563134
## GSM4462297 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563133
## GSM4462298 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563132
## GSM4462299 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563131
## GSM4462300 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563123
## GSM4462301 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563122
## GSM4462302 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563121
## GSM4462303 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563120
## GSM4462304 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563119
## GSM4462305 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14563118
## relation.1
## GSM4462262 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086060
## GSM4462263 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086061
## GSM4462264 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086062
## GSM4462265 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086063
## GSM4462266 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086064
## GSM4462267 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086065
## GSM4462268 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086066
## GSM4462269 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086067
## GSM4462270 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086068
## GSM4462271 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086069
## GSM4462272 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086070
## GSM4462273 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086071
## GSM4462274 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086072
## GSM4462275 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086073
## GSM4462276 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086074
## GSM4462295 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086093
## GSM4462296 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086094
## GSM4462297 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086095
## GSM4462298 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086096
## GSM4462299 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086097
## GSM4462300 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086098
## GSM4462301 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086099
## GSM4462302 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086100
## GSM4462303 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086101
## GSM4462304 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086102
## GSM4462305 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8086103
## supplementary_file_1
## GSM4462262 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462262/suppl/GSM4462262_20191029.A-full_intein_uppest5_RFP_1_abundance.tsv.gz
## GSM4462263 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462263/suppl/GSM4462263_20191029.A-full_intein_uppest5_RFP_2_abundance.tsv.gz
## GSM4462264 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462264/suppl/GSM4462264_20191029.A-full_intein_uppest5_RFP_3_abundance.tsv.gz
## GSM4462265 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462265/suppl/GSM4462265_20191029.A-c-intein_RFP_control_uppest5_RFP_1_abundance.tsv.gz
## GSM4462266 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462266/suppl/GSM4462266_20191029.A-c-intein_RFP_control_uppest5_RFP_2_abundance.tsv.gz
## GSM4462267 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462267/suppl/GSM4462267_20191029.A-c-intein_RFP_control_uppest5_RFP_3_abundance.tsv.gz
## GSM4462268 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462268/suppl/GSM4462268_20191029.A-GFP_spCas_uppest5_1_abundance.tsv.gz
## GSM4462269 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462269/suppl/GSM4462269_20191029.A-GFP_spCas_uppest5_2_abundance.tsv.gz
## GSM4462270 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462270/suppl/GSM4462270_20191029.A-GFP_spCas_uppest5_3_abundance.tsv.gz
## GSM4462271 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462271/suppl/GSM4462271_20191029.A-GFP_saCas_uppest5_1_abundance.tsv.gz
## GSM4462272 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462272/suppl/GSM4462272_20191029.A-GFP_saCas_uppest5_2_abundance.tsv.gz
## GSM4462273 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462273/suppl/GSM4462273_20191029.A-GFP_saCas_uppest5_3_abundance.tsv.gz
## GSM4462274 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462274/suppl/GSM4462274_20191029.A-GFP_ctrl_uppest5_1_abundance.tsv.gz
## GSM4462275 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462275/suppl/GSM4462275_20191029.A-GFP_ctrl_uppest5_2_abundance.tsv.gz
## GSM4462276 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462276/suppl/GSM4462276_20191029.A-GFP_ctrl_uppest5_3_abundance.tsv.gz
## GSM4462295 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462295/suppl/GSM4462295_20200320.A-HEK_1high_rep1_abundance.tsv.gz
## GSM4462296 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462296/suppl/GSM4462296_20200320.A-HEK_2_rep1_abundance.tsv.gz
## GSM4462297 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462297/suppl/GSM4462297_20200320.A-HEK_3_rep1_abundance.tsv.gz
## GSM4462298 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462298/suppl/GSM4462298_20200320.A-HEK_4_rep1_abundance.tsv.gz
## GSM4462299 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462299/suppl/GSM4462299_20200320.A-HEK_1high_rep2_abundance.tsv.gz
## GSM4462300 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462300/suppl/GSM4462300_20200320.A-HEK_2_rep2_abundance.tsv.gz
## GSM4462301 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462301/suppl/GSM4462301_20200320.A-HEK_3_rep2_abundance.tsv.gz
## GSM4462302 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462302/suppl/GSM4462302_20200320.A-HEK_4_rep2_abundance.tsv.gz
## GSM4462303 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462303/suppl/GSM4462303_20200320.A-HEK_1high_rep3_abundance.tsv.gz
## GSM4462304 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462304/suppl/GSM4462304_20200320.A-HEK_2_rep3_abundance.tsv.gz
## GSM4462305 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4462nnn/GSM4462305/suppl/GSM4462305_20200320.A-HEK_3_rep3_abundance.tsv.gz
## cell line/strain:ch1 cell/sample type:ch1 genotype/variation:ch1
## GSM4462262 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462263 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462264 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462265 HEK293T cell lysate RFP
## GSM4462266 HEK293T cell lysate RFP
## GSM4462267 HEK293T cell lysate RFP
## GSM4462268 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462269 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462270 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462271 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462272 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462273 HEK293T cell lysate saKKH-CBE3 + GFP
## GSM4462274 HEK293T cell lysate GFP
## GSM4462275 HEK293T cell lysate GFP
## GSM4462276 HEK293T cell lysate GFP
## GSM4462295 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462296 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462297 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462298 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462299 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462300 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462301 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462302 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462303 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462304 HEK293T cell lysate saKKH-CBE3 + RFP
## GSM4462305 HEK293T cell lysate saKKH-CBE3 + RFP
## time point:ch1 treatment/method:ch1
## GSM4462262 72h Plasmid transfection
## GSM4462263 72h Plasmid transfection
## GSM4462264 72h Plasmid transfection
## GSM4462265 0 Plasmid transfection
## GSM4462266 0 Plasmid transfection
## GSM4462267 0 Plasmid transfection
## GSM4462268 72h Plasmid transfection
## GSM4462269 72h Plasmid transfection
## GSM4462270 72h Plasmid transfection
## GSM4462271 72h Plasmid transfection
## GSM4462272 72h Plasmid transfection
## GSM4462273 72h Plasmid transfection
## GSM4462274 0 Plasmid transfection
## GSM4462275 0 Plasmid transfection
## GSM4462276 0 Plasmid transfection
## GSM4462295 48h mRNA transfection
## GSM4462296 48h mRNA transfection
## GSM4462297 48h mRNA transfection
## GSM4462298 48h mRNA transfection
## GSM4462299 48h mRNA transfection
## GSM4462300 48h mRNA transfection
## GSM4462301 48h mRNA transfection
## GSM4462302 48h mRNA transfection
## GSM4462303 48h mRNA transfection
## GSM4462304 48h mRNA transfection
## GSM4462305 48h mRNA transfection# Tambien podemos usar estas funciones iterativas en pipes
# para obtener el nombre de objetos en cada experimento
map(data, experimentData) %>% map(slotNames)## $`GSE148349-GPL24247`
## [1] "name" "lab" "contact"
## [4] "title" "abstract" "url"
## [7] "pubMedIds" "samples" "hybridizations"
## [10] "normControls" "preprocessing" "other"
## [13] ".__classVersion__"
##
## $`GSE148349-GPL24676`
## [1] "name" "lab" "contact"
## [4] "title" "abstract" "url"
## [7] "pubMedIds" "samples" "hybridizations"
## [10] "normControls" "preprocessing" "other"
## [13] ".__classVersion__"Existen formas más eficientes que las pipes para hacer fujos de trabajo, especialmente si los reutilizamos a menudo. La forma base es describir una función, con fun <- function(x){hacer algo a x}. Esto puede añadir una capa de complejidad, dado que es necesario incluir variables intermedias para cada transformación de los datos, y además resulta largo de escribir. Utilizando purr::compose() podemos crear una función similar a un pipe, que aplica sucesivamente las funciones de la composición al objeto que le pasemos.
# Creando una función con compose(fun1, fun2, ...)
# esta eliminará los valores vacios (NA) de una lista
not_a_na <- purrr::compose(na.omit , as.character)
A <- c(NA,'ddd','dgrfg',NA) # Un vector de demostración
A %>% na.omit %>% as.character # Forma tradicional con pipes## [1] "ddd" "dgrfg"## [1] "ddd" "dgrfg"
## attr(,"na.action")
## [1] 1 4
## attr(,"class")
## [1] "omit"Considerando que en un meta-analisis comparamos datasets de multiples estudios, estos deben ser de un mismo organismo para que la comparación sea valida.
# Usamos una función de biobase para extraer data de fenotipos
list.of.phenoData <- map(data, pData)
# Si queremos extraer la data de cuales son los organismos necesitamos
# la columna dentro de la tabla de datasets con esa información
list.of.phenoData %>% map(names) %>% # Toma los nombres con names()
map(~str_extract(.,'org.*')) %>% # Deja solo las entradas con org...
map(not_a_na) -> my.organism.entry # Elimina las entradas vacias y guardaUna forma más rapida es utilizar purrr::pluck(), que actua como un [['indice']] recursivo hasta encontrar el 'indice' que buscamos.
## $`GSE148349-GPL24247`
## [1] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [6] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [11] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [16] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [21] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [26] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [31] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
## [36] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus"
##
## $`GSE148349-GPL24676`
## [1] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## [6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## [11] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## [16] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## [21] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## [26] "Homo sapiens"Desde ensembl_transcript_ID hasta EC number, para reconstruir redes.
my.GEOfile = GEOquery::getGEOfile('GSE148349',AnnotGPL = T, destdir = getwd())
GEOquery::getGEO(filename=my.GEOfile) -> soft
suppfiles = GEOquery::getGEOSuppFiles('GSE148349')
suppfiles %>% row.names() -> full.path.raw_tar
full.path.raw_tar %>% str_match('GSE\\d+.RAW.*')
full.path.raw_tar %>% str_match('.*(?=GSE\\d+.RAW.*)') -> gse.folder
untar(tarfile = full.path.raw_tar ,exdir = gse.folder)my.gunzip <- function(a.file){GEOquery::gunzip(a.file,remove = T, overwrite = T)}
get.my.gz.files <- function(gsefolder)
{
gsefolder %>% list.files(full.names = T ) %>%
str_extract('.*gz') %>% na.cleaner %>% map(my.gunzip)
}
# TODO: evitar que descargue mil veces
gse.folder %>% get.my.gz.files
gse.folder %>% list.files(full.names = T ) %>% str_extract('.*tsv$') %>% na.cleaner -> tsv.files.path
#Función anónima
tsv.files.path %>%
map(function(files.path00)
{
readr::read_delim(files.path00, delim = '\t', skip = 0,col_names = TRUE)
}) -> df_list #
df_list %>% class
df_list %>% length
df_list %>% namestsv.files.path %>% str_extract('GSM\\d+') -> gsm.names
df_list %<>% purrr::set_names(gsm.names)
df_list %>% names
df_list['GSM4462281']# Convocando la API de KEGG
BiocManager::install("KEGGREST")
library("KEGGREST") # API que permite acceder a data de KEGG programaticamente
# Que hace esto?
listDatabases()
#my.EC <- c('1.8.1.4')#, '2.7.4.12', '', '2.7.4.13', '2.7.4.9', '2.7.4.9')
#keggFind("genes", my.EC) %>% as.matrix() %>% rownames() %>%keggGet() -> found.kegg
#keggFind("genes",'1738')
#keggFind("genome",'ENSG00000091140')ensembl <- useMart("ensembl") #para toda la base de datos
Hs.ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl") #solo Humano
searchAttributes(mart = Hs.ensembl, pattern = 'GO')my.genes <- c('ENSG00000091140') #GENE como ejemplo
my.genes.symbols <- getBM(
attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene_id','goslim_goa_description'),filters ='ensembl_gene_id',values = my.genes,mart = Hs.ensembl)
my.genes.symbolsmy.genes <- c('ENST00000487058',all.commom.genes %>% sample(8), 'ENST00000535366')
my.genes.symbols <- getBM(
attributes=c('ensembl_transcript_id','hgnc_symbol','entrezgene_id','wikigene_description','goslim_goa_description'),filters ='ensembl_transcript_id',values = my.genes,mart = Hs.ensembl)
my.genes.symbolsna.cleaner <- purrr::compose(as.character, na.exclude)
my.genes.symbols$entrezgene_id %>% unique %>% na.cleaner %>% paste0('hsa:',.) %>% keggGet -> my.kegg.list
my.kegg.list %>% length
my.kegg.list %>% names
my.genes.symbols$hgnc_symbol[!is.na(my.genes.symbols$entrezgene_id)] %>% unique -> mis.nombres
my.kegg.list %>% purrr::set_names(mis.nombres) -> my.kegg.info
my.kegg.info %>% names
my.kegg.info[["ENO2"]] %>% class
map( my.kegg.info, pluck('PATHWAY')) %>% glimpse()
map( my.kegg.info, pluck('PATHWAY')) %>% purrr::compact() FONDECYT Postdoctoral Fellow, Universidad de Chile, deepen.data@gmail.com↩︎
Pregrado, Universidad de Chile↩︎