18 Mouse Samples

CTL and TRT3

basic analysis, see what PCA plots look like and DEGs

coldata
##         treatment
## DZLA_18       CTL
## DZLA_1        CTL
## DZLA_20      TRT3
## DZLA_21       CTL
## DZLA_22       CTL
## DZLA_23       CTL
## DZLA_24      TRT3
## DZLA_26      TRT3
## DZLA_27       CTL
## DZLA_2        CTL
## DZLA_3        CTL
## DZLV_13      TRT3
## DZLV_14      TRT3
## DZLV_15      TRT3
## DZLV_4       TRT3
## DZLV_5       TRT3
## DZLV_6       TRT3
## DZLV_7       TRT3

Alignment quality

Pre batch correction: heatmap and PCA

Post batch correction: heatmap and PCA

Comparisons

1. TRT3 vs CTL

Differentially expressed genes

Up-regulated Down-regulated Total
TRT3 vs CTL 1146 1161 2307

Volcano plot

1. TRT3 vs CTL, padj<0.05, |FC|>1

KEGG and GO