Hi, I was doing RNAseq for CD31 selected human endothelial cells. Unfortunately, My cells didn't express CD31. I don't know why. The RNAseq method is SMART-Seq Stranded Kit (Takara).
I followed the general pipeline, Quality Control-Cutadapt-HISAT2-Stringtie. For the Stringtie, I used the reference file (hg19) to guide assembly.
For the gene abundance estimate of the Stringtie, the CD31(PECAM1) expression(FPKM) is 0.
Has anyone ever met this problem? What's the possible issue? Thanks.