title: RNA-Seq analysis of LYN deficient HS-5 stroma cells cocultured with primary human CLL cells
design: RNA-Seq analysis of LYN deficient HS-5 stroma cells cocultured with primary human CLL cells
library_construction_protocol: LYN WT and LYN KO cells (2 clones per genotype) were cultured with primary CLL patient samples (3 different patients) for 72h. CLL cells were removed, feeder layers washed carefully before trypsinization and subsequently contaminating CLL cells were removed by magnetic depletion of CD45+ cells using human CD45 MojoSort reagents (Biolegend) according to the manufacturer's instructions.  mRNA was isolated HS-5 cells using the RNeasy plus kit (Qiagen) according to the manufacturer's instructions and RNA quantity and quality was examined by NanoDrop1000 (Thermo Scientific) spectrometric measurement.  Samples were processed and sequenced PE100, 50M reads per sample at the Cologne Center for Genomics according to in-house standards.