title: Illumina HiSeq 2000 paired end sequencing; Bulk RNA-seq for cervix tissue and HPV16 infected human W12 cervical cell lines
design: Bulk RNA-seq for cervix tissue and HPV16 infected human W12 cervical cell lines
library_construction_protocol: W12 cells were cultured in a monolayer to restrict cell differentiation and maintain the phenotype of the basal epithelial. Cells were collected at the lowest possible passage after cloning (p3 to p8) to minimise any effects of genomic instability caused byderegulated HPV16 oncogenes.   Cells were lysed on ice for 30 minutes in 50 ml freshly prepared icecold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet (Roche complete, EDTA-free)). Total RNA was isolated and subjected to Ribo-Zero rRNA depletion and DNAse treatment.  cDNA libraries were prepared from the ribo-depleted RNA with the TruSeqâ„¢ RNA and DNA Sample Prep Kit (Illumina)