GSE201174
Chakkapong_Burudpakdee
2024-08-10
GSE201174 -Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies
Public on Dec 31, 2022
Comparative gene expression profiling analysis of RNA-seq data for CAR-Macrophage and WT-Macrophage cells with and without CHLA-neuroblastoma co-culture
NextSeq 2000 (Homo sapiens) Bulk RNAseq
Morgridge Institute for Research
Zhang J, Steill J
We generate macrophages from pluripotent stem cells (PSCs) with GD2 CARs integrated into AAVS1 locus. To produce CAR macrophages (CAR-M) we established a serum- and feeder-free differentiation protocol which generates macrophages through arterialized hemogenic endothelium.
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## select## CAR.M_1 CAR.M_2 CAR.M_3 WT.M.CHLA_1 WT.M.CHLA_2 WT.M.CHLA_3
## A1BG 69 548 396 43 686 462
## A1BG-AS1 151 169 201 0 83 2
## A1CF 0 1 1 0 0 1
## A2M 20595 22922 33978 14435 72483 74842
## A2M-AS1 153 227 0 0 117 103
## A2ML1 0 0 0 4 0 0
## CAR.M.CHLA_1 CAR.M.CHLA_2 CAR.M.CHLA_3
## A1BG 61 171 317
## A1BG-AS1 1 427 226
## A1CF 0 0 1
## A2M 24809 56728 63225
## A2M-AS1 0 104 173
## A2ML1 0 1 0## converting counts to integer mode## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates: 22 workers
## mean-dispersion relationship
## final dispersion estimates, fitting model and testing: 22 workers## Warning: Ignoring 12027 observations## Warning: Removed 10125 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')## Warning: Data is of class data.frame. Coercing to dgCMatrix.##
## CAR.M CAR.M.CHLA WT.M.CHLA
## 3 3 3## Normalizing layer: counts
## Finding variable features for layer counts
## Centering and scaling data matrix## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.## PC_ 1
## Positive: HRK, CERKL, PDP2, LINC02517, VSIG1, FAM74A7, SNX22, ANGPT2, PCDH11Y, MFSD2B
## LINC00598, NLRP12, PTCHD4, ADGRF2, ERVV-1, RNA45SN1, FAM71F2, SLC28A1, TAGLN, SLC8A1-AS1
## MAN1B1-DT, ELMOD1, SLC36A2, PCDHB9, CCDC142, PCAT7, ZNF793, TYW1B, ZFP91-CNTF, EDNRB-AS1
## Negative: ARL6IP5, FLI1, FBXO11, OXSR1, ZNF217, ERBIN, GOLGA5, GLYR1, HMGCR, KDM3B
## SDCBP, DOCK10, ACBD5, PDHB, HNRNPR, ANKRD13C, NR3C1, ACAP2, PRKAR1A, CD2AP
## MFAP1, SEC22B, OSBPL11, DLD, TXNRD1, RACGAP1, LIPA, SH2B3, SP3, TOP2B
## PC_ 2
## Positive: TNFSF15, SPP1, FLNA, UHRF1, VAV2, SERPINA1, TMEM176B, RASA4, TFRC, IGFBP3
## WDR76, A2M, BHLHE41, MCM3, CYBB, LTBP2, STK32B, NEFM, CASK, CDCP1
## ARAP2, OPN3, LIMA1, CRIM1, TIMP1, NES, VDR, CDC6, SHOX2, RNA28SN5
## Negative: ITGB7, RBP1, DEFA1, DEFA1B, FCER1A, LY6E, PRG2, SLC47A1, TCN2, RETN
## CYP2S1, EPX, LGALS3BP, HS3ST2, PDK4, CLC, RNASE2, NCF2, HP, SELPLG
## SEMA4A, PLIN2, POLR2J2, PRG3, ANXA6, BLVRB, PADI2, SDS, PMF1-BGLAP, HMOX1
## PC_ 3
## Positive: SMYD3, CD93, PRDX4, RGPD5, LHFPL2, OLFML3, GPNMB, GPR34, TMEM273, SUCNR1
## RBBP7, ANKH, SMS, TLR7, BCAT1, RARRES2, UTP4, HLA-DPA1, PRKACB, KIAA1671
## ALG13, FAM174B, MBOAT1, SLC1A3, GAB1, TAL1, GBE1, DCAKD, SLFN11, NLRP2
## Negative: ANPEP, NCF1, NEAT1, G0S2, PTPN13, TNFRSF4, TTC39B, EHD1, MMP25, MAP3K14
## ABLIM1, HJURP, TIFAB, NPIPB5, CKAP2L, TACC3, LAMB3, GP1BA, MYCL, LILRB2
## SLC38A1, TPD52, VCAM1, TIMP3, ADAM8, FFAR2, ZNF558, MMP9, TUBB2B, GMPR
## PC_ 4
## Positive: SGO1, MYSM1, LRCH3, MEFV, LIX1L-AS1, PPAN, KAT6B, STRN3, NPIPA1, EZH2
## ZNF580, NDUFC2, NEK2, BRD2, EIF2B2, SPRY4, TMEM126B, CALD1, NBPF8, STAG3L3
## GCNT1, NR4A1, SMC3, AKAP6, CWC22, KMT5A, NBPF14, GOLGA4, TGFB2-OT1, ITSN2
## Negative: IER3-AS1, ITGAD, POLR2J4, DGKG, WASH8P, NDUFC2-KCTD14, NPHP3-ACAD11, RNA18SN4, RNA18SN2, RNA18SN3
## ADGRF5, SNORA100, PCGF2, P2RY11, SIK1, VASH1-AS1, SMN2, DGCR11, CPXM1, RNASEK-C17orf49
## GPR89B, PRKCZ, POLA1, TRIM39-RPP21, NSFP1, TRIM6-TRIM34, SELENOI, NEDD8, GDPGP1, KIF5C
## PC_ 5
## Positive: PRPF40B, UBE2F-SCLY, LRRC37A2, MTFR2, YPEL3, STAG3L1, GIN1, NXF3, ZNHIT2, LINC01303
## RN7SK, ZC2HC1A, NPPA-AS1, LRRC24, SMIM2-AS1, TSPAN18, HOXB7, MAP1LC3B2, OGG1, RNF139-AS1
## LXN, NEURL4, TRPT1, SFSWAP, TREM1, CCDC137, IL2RA, NCF1B, EIF2S3B, IFT74
## Negative: OTOA, HTRA4, FPR2, C1QL3, CAMP, FAM133DP, SELL, RAD51L3-RFFL, VCAN, IKZF2
## WDTC1, KCNE3, GPR27, NRBF2, ALK, LRIG2, RNF141, SETDB2, ITPR3, CAB39L
## NUDT4, RNFT1, TNFSF12-TNFSF13, TMCC3, CIDEB, CORO7-PAM16, FAM47E-STBD1, ABALON, SARM1, MEGF9## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning: Requested number is larger than the number of available items (9).
## Setting to 9.
## Warning in ElbowPlot(data): The object only has information for 8 reductions
##
## CAR.M CAR.M.CHLA WT.M.CHLA
## 3 3 3## PC_1 PC_2 PC_3 PC_4 PC_5 PC_6
## CAR.M_1 9.514085 -31.98310 1.023255 -3.292667 18.6988295 1.2477944
## CAR.M_2 1.115779 -17.21792 2.213481 -0.243182 -12.4682849 -19.2794144
## CAR.M_3 -16.332880 -18.39174 6.586399 7.528124 -14.2678227 15.7583987
## WT.M.CHLA_1 53.407321 11.03628 -5.366924 16.075148 -2.0161509 2.1894910
## WT.M.CHLA_2 2.269122 13.35734 18.930037 -7.694567 4.7536209 0.2117183
## WT.M.CHLA_3 -2.390333 15.62724 23.380213 -9.971425 -0.5539547 0.4422073
## PC_7 PC_8
## CAR.M_1 -2.1457165 1.6992670
## CAR.M_2 0.5441645 -2.9641750
## CAR.M_3 1.7884107 1.2911808
## WT.M.CHLA_1 -1.0129044 0.6258434
## WT.M.CHLA_2 16.1019785 -2.2444104
## WT.M.CHLA_3 -14.1778000 1.3733786
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