13 Mouse Samples

DFF is the controls and CKO is the mutant.

basic analysis, see what PCA plots look like and DEGs

coldata
##      treatment sex group
## dn15       DFF   F DFF_F
## dq2        DFF   M DFF_M
## dq7        DFF   M DFF_M
## dq8        DFF   F DFF_F
## dz11       CKO   F CKO_F
## dz8        CKO   F CKO_F
## eb3        DFF   M DFF_M
## ep2        CKO   M CKO_M
## fk1        CKO   M CKO_M
## fk5        CKO   F CKO_F
## fn2        CKO   M CKO_M
## fn3        CKO   F CKO_F
## fn8        DFF   F DFF_F

Alignment quality

Pre batch correction: heatmap and PCA

Post batch correction: heatmap and PCA

Comparisons

1. CKO vs DFF

2. CKO_F vs DFF_F

3. CKO_M vs DFF_M

Differentially expressed genes

Up-regulated Down-regulated Total
CKO vs DFF 19 36 55
CKO_F vs DFF_F 161 296 457
CKO_M vs DFF_M 181 95 276

Volcano plot

1. CKO vs DFF, padj<0.1, FC>1.5

2. CKO_F vs DFF_F, padj<0.1, FC>1.5

3. CKO_M vs DFF_M, padj<0.1, FC>1.5

KEGG and GO