RNA-Seq of a patient-derived tumor cell line: pediatric undifferentiated sarcoma
To construct the RNA sequencing library, we isolated RNA from tissue or cell line samples and selected for poly(A)-enriched RNA. The RNA was fragmented, treated with DNase, and dephosphorylated. These RNA fragments were purified and the sample underwent RNA hydrolysis, ssDNA adapter ligation to the 3' end, followed by PCR enrichment. We then size selected the RNA molecules and sequenced them on a HiSeq 2500.
alignment_software
TopHat v1.4.1