Last updated: 2023-03-17

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Knit directory: NIVI_HIPEC3_BF/

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Aim of the test data

Exploratory analysis to check the CTG readouts requested by Suad

Researcher

ML/Suad/Niv

Readout

CTG values

Required R packages

here, ggplot2, ggpubr, tidyverse,

[1] "/home/mli/ML_CampbellLab/230304_Suad_test/NIVI_HIPEC3_BF"

Screen details

Screen date (yyyy-mm-dd)

2023-02-24 seed then carried to 2023-03-06 BF imaging daily
***

Known technical issues

Cell density inconsistent for certain cell types, cell counting might not be accurate.

For the plate 43C bottom half, Org66 did not have enough cells so it missed out SN38 1uM (3 wells) and SN38 5uM (2 wells).


Experiment details

Cell seeding conditions:
80% Matrigel base layer
50% Matrigel embedding layer
1500 cells seeded per well

Cell culture conditions:

day3:pre-treatment
day4: day of treatment, images taken before adding the drugs
day7: endpoint 1 (removed the drugs but kept on imaging until d10, CTG assay on d10)
day10: endpoint 2

Image Formatting and Preprocessing

The raw CTG data was read into R Studio.

Example of ilastik generated probability mask (colored) overlayed to BF images

Preprocessing layout meta-data and CTG data

Assay quality check

This is only for reference as we only had 1 plate per cell type per condition %CV and Z prime numbers are not powerful as they are in a screen setting Still it shows us the variability etc.

CTG Normalised values

CTG value is normalised to median values in DMSO wells per plate per cell type

Calculate summary statistics

Boxplot of Normalised CTG



 

Analysed by Mark Li

Victorian Centre for Functional Genomics

 


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] readxl_1.4.2      data.table_1.14.8 ggpubr_0.6.0      htmltools_0.5.4  
 [5] here_1.0.1        forcats_1.0.0     stringr_1.5.0     dplyr_1.1.0      
 [9] purrr_1.0.1       readr_2.1.4       tidyr_1.3.0       tibble_3.1.8     
[13] ggplot2_3.4.1     tidyverse_1.3.2   DT_0.27           workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] fs_1.6.1            lubridate_1.9.2     RColorBrewer_1.1-3 
 [4] httr_1.4.4          rprojroot_2.0.3     tools_4.2.0        
 [7] backports_1.4.1     bslib_0.4.2         utf8_1.2.3         
[10] R6_2.5.1            platetools_0.1.5    DBI_1.1.3          
[13] colorspace_2.1-0    withr_2.5.0         tidyselect_1.2.0   
[16] processx_3.8.0      compiler_4.2.0      git2r_0.31.0       
[19] textshaping_0.3.6   cli_3.6.0           rvest_1.0.3        
[22] formatR_1.14        xml2_1.3.3          labeling_0.4.2     
[25] sass_0.4.5          scales_1.2.1        callr_3.7.3        
[28] systemfonts_1.0.4   digest_0.6.31       rmarkdown_2.20     
[31] pkgconfig_2.0.3     highr_0.10          dbplyr_2.3.0       
[34] fastmap_1.1.0       htmlwidgets_1.6.1   rlang_1.0.6        
[37] rstudioapi_0.14     farver_2.1.1        jquerylib_0.1.4    
[40] generics_0.1.3      jsonlite_1.8.4      crosstalk_1.2.0    
[43] car_3.1-1           googlesheets4_1.0.1 magrittr_2.0.3     
[46] Rcpp_1.0.10         munsell_0.5.0       fansi_1.0.4        
[49] abind_1.4-5         lifecycle_1.0.3     stringi_1.7.12     
[52] whisker_0.4.1       yaml_2.3.7          carData_3.0-5      
[55] grid_4.2.0          promises_1.2.0.1    crayon_1.5.2       
[58] haven_2.5.1         hms_1.1.2           knitr_1.42         
[61] ps_1.7.2            pillar_1.8.1        ggsignif_0.6.4     
[64] reprex_2.0.2        glue_1.6.2          evaluate_0.20      
[67] getPass_0.2-2       modelr_0.1.10       vctrs_0.5.2        
[70] tzdb_0.3.0          httpuv_1.6.9        cellranger_1.1.0   
[73] gtable_0.3.1        assertthat_0.2.1    cachem_1.0.6       
[76] xfun_0.37           mime_0.12           broom_1.0.3        
[79] rstatix_0.7.2       later_1.3.0         ragg_1.2.5         
[82] googledrive_2.0.0   gargle_1.3.0        timechange_0.2.0   
[85] ellipsis_0.3.2