Bulk RNA seq for cultured human CB with shRNAs, hg38

sample treatment name
41_1 shRen 41R1
41_2 shRen 41R2
41_3 shRen 41R3
65_1 shJARID2#2 65R1
65_2 shJARID2#2 65R2
65_3 shJARID2#2 65R3
82_1 shEZH2#2 82R1
82_2 shEZH2#2 82R2
82_3 shEZH2#2 82R3 
coldata
##            treatment
## shRenR1        shRen
## shRenR2        shRen
## shRenR3        shRen
## shJARID2R1  shJARID2
## shJARID2R2  shJARID2
## shJARID2R3  shJARID2
## shEZH2R1      shEZH2
## shEZH2R2      shEZH2
## shEZH2R3      shEZH2

Alignment quality

heatmap and PCA

Comparisons

shJARID2 vs shRen

shJARID2 vs shEZH2

shRen vs shEZH2

Differentially expressed genes

high in 1st high in 2nd Total
shJARID2 vs shRen 734 640 1374
shJARID2 vs shEZH2 1266 669 1935
shRen vs shEZH2 1230 702 1932

Volcano plot

padj<0.05, |FC|>2

KEGG and GO