Hello! I really appreciate it if anyone can help me with this issue!
Recently we used siRNA to knock down a gene, and did RNA-seq to find the downstream targets of this gene. We performed qRT-PCR and Western blot to make sure the gene was successfully knocked down before submitting it to sequencing. But when we check the RNA-seq results, this weird thing happened... The expression of this gene was not reduced - both the ctrl and treatment group have ~90 counts of this gene.
I used both STAR and HISAT2 for alignment, followed by DESeq2 normalization, but both of them generated similar results.
Thanks so much if you could provide any suggestions!