RNAseq Results Table of SNRPB and SNRPN expressing HEK cells
Abstract
This dataset contains stranded poly(A)+ RNA sequencing data generated from isogenic HEK293 Flp-In™ T-REx™ cell lines expressing either SNRPB or SNRPN from a single-copy, doxycycline-inducible cDNA transgene (C-terminal HA-mNeonGreen). Endogenous SNRPB was deleted by CRISPR/Cas9 after transgene integration, yielding cell lines that rely exclusively on the transgenic isoform. For clarity, SNRPB-only clones are designated “BKO<cloneID>”, and SNRPN-only clones are designated “NKO<cloneID>”, where <cloneID> corresponds to the unique clone identifier for each line.
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Sample to sample distances 1922_N_KO11_Cyclo_rep2 2124_N_KO13_Cyclo_rep4 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 0104_N_KO6_EtOH_rep1 0811_N_KO12_EtOH_rep3 0710_N_KO11_EtOH_rep2 0912_N_KO13_EtOH_rep4 28_HEK_EtOH_rep4 29_HEK_EtOH_rep5 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep3 30_HEK_EtOH_rep6 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 1922_N_KO11_Cyclo_rep2 2124_N_KO13_Cyclo_rep4 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 0104_N_KO6_EtOH_rep1 0811_N_KO12_EtOH_rep3 0710_N_KO11_EtOH_rep2 0912_N_KO13_EtOH_rep4 28_HEK_EtOH_rep4 29_HEK_EtOH_rep5 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep3 30_HEK_EtOH_rep6 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 cell_line rep1 rep1_2 rep2 replicate 1 2 3 4 5 6 group B_KO_EtOH N_KO_EtOH B_KO_Cyclo N_KO_Cyclo control 0 10 20 30 40 50 60 70
Sample to sample distances (diagonal set to NA) 1922_N_KO11_Cyclo_rep2 2124_N_KO13_Cyclo_rep4 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 0104_N_KO6_EtOH_rep1 0811_N_KO12_EtOH_rep3 0710_N_KO11_EtOH_rep2 0912_N_KO13_EtOH_rep4 28_HEK_EtOH_rep4 29_HEK_EtOH_rep5 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep3 30_HEK_EtOH_rep6 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 1922_N_KO11_Cyclo_rep2 2124_N_KO13_Cyclo_rep4 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 0104_N_KO6_EtOH_rep1 0811_N_KO12_EtOH_rep3 0710_N_KO11_EtOH_rep2 0912_N_KO13_EtOH_rep4 28_HEK_EtOH_rep4 29_HEK_EtOH_rep5 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep3 30_HEK_EtOH_rep6 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 cell_line rep1 rep1_2 rep2 replicate 1 2 3 4 5 6 group B_KO_EtOH N_KO_EtOH B_KO_Cyclo N_KO_Cyclo control 30 40 50 60 70
Normalized expression values of 40 most variable genes 1922_N_KO11_Cyclo_rep2 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 2124_N_KO13_Cyclo_rep4 0710_N_KO11_EtOH_rep2 0104_N_KO6_EtOH_rep1 0811_N_KO12_EtOH_rep3 0912_N_KO13_EtOH_rep4 27_HEK_EtOH_rep3 28_HEK_EtOH_rep4 29_HEK_EtOH_rep5 30_HEK_EtOH_rep6 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 HSPA8 CEBPE HSPA1B LCP1 ANOS1 PYCR1 ZNF22 H2AC6 NOG ATOH8 ENSG00000287814 ENSG00000287453 VPS9D1−AS1 MIR4458HG ENSG00000272004 DDX19B P2RX5 ZNF525 ZNF320 NECTIN3−AS1 LRRN1 SALL3 ZNF600 PPP2R2B SYT1 CHRDL1 SPARC TSTD1 DECR1 LINC00839 ZNF738 ZNF610 LRRC7 NECTIN3 ZNF257 ZNF727 LINC02506 COL3A1 ENSG00000289069 KC6 cell_line rep1 rep1_2 rep2 replicate 1 2 3 4 5 6 group B_KO_EtOH N_KO_EtOH B_KO_Cyclo N_KO_Cyclo control 4 6 8 10 12 14
Normalized expression values of 40 genes with highest mean 1922_N_KO11_Cyclo_rep2 1316_N_KO6_Cyclo_rep1 2023_N_KO12_Cyclo_rep3 2124_N_KO13_Cyclo_rep4 15_B_KO18_Cyclo_rep2 18_B_KO18_Cyclo_rep4 14_B_KO11_Cyclo_rep1 17_B_KO11_Cyclo_rep3 0104_N_KO6_EtOH_rep1 0710_N_KO11_EtOH_rep2 0811_N_KO12_EtOH_rep3 0912_N_KO13_EtOH_rep4 28_HEK_EtOH_rep4 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep3 30_HEK_EtOH_rep6 02_B_KO11_EtOH_rep1 05_B_KO11_EtOH_rep3 29_HEK_EtOH_rep5 03_B_KO18_EtOH_rep2 06_B_KO18_EtOH_rep4 MT−CO1 XIST EEF1A1 MT−CO2 MT−RNR2 MT−ND4 EEF2 GAPDH HSP90AA1 MT−CO3 ENO1 ACTG1 RPS4X RPL4 RPS2 MT−CYB MT−ATP6 MT−ND5 RACK1 PKM CKB RPL7A RPL13 RPLP0 NPM1 TUBB IRS4 MT−ND1 YBX1 RPL6 HSP90AB1 MT−ND2 ACTB RPL8 RPS8 HNRNPA1 TUBA1B HNRNPU RPL15 RPS16 cell_line rep1 rep1_2 rep2 replicate 1 2 3 4 5 6 group B_KO_EtOH N_KO_EtOH B_KO_Cyclo N_KO_Cyclo control 15.5 16 16.5 17 17.5 18 18.5
02_B_KO11_EtOH_rep1 03_B_KO18_EtOH_rep2 05_B_KO11_EtOH_rep3 06_B_KO18_EtOH_rep4 0104_N_KO6_EtOH_rep1 0710_N_KO11_EtOH_rep2 0811_N_KO12_EtOH_rep3 0912_N_KO13_EtOH_rep4 14_B_KO11_Cyclo_rep1 15_B_KO18_Cyclo_rep2 17_B_KO11_Cyclo_rep3 18_B_KO18_Cyclo_rep4 1316_N_KO6_Cyclo_rep1 1922_N_KO11_Cyclo_rep2 2023_N_KO12_Cyclo_rep3 2124_N_KO13_Cyclo_rep4 25_HEK_EtOH_rep1 26_HEK_EtOH_rep2 27_HEK_EtOH_rep328_HEK_EtOH_rep4 29_HEK_EtOH_rep5 30_HEK_EtOH_rep6 −10 0 10 −10 0 10 PC1: 47% variance PC2: 36% variance group B_KO_Cyclo B_KO_EtOH control N_KO_Cyclo N_KO_EtOH
1e−01 1e+00 1e+01 1e+02 1e+03 1e+04 1e+05 −3 −2 −1 0 1 2 3 BKOEtOH.vs.Ctrl mean of normalized counts log fold change
1e−01 1e+00 1e+01 1e+02 1e+03 1e+04 1e+05 −3 −2 −1 0 1 2 3 NKOEtOH.vs.Ctrl mean of normalized counts log fold change
1e−01 1e+00 1e+01 1e+02 1e+03 1e+04 1e+05 −3 −2 −1 0 1 2 3 BKOEtOH.vs.NKOEtOH mean of normalized counts log fold change
1e−01 1e+00 1e+01 1e+02 1e+03 1e+04 1e+05 −3 −2 −1 0 1 2 3 BKOEtOH.vs.BKOCyclo mean of normalized counts log fold change