MP12
Preparation of RNA-seq libraries and sequencing Five µg total RNA extracted from 7 highly Nef-dependent  cell lines (JTAg, Jurkat E6.1, bl41, Ramos, CEM A301, CEM SS and HSB2) and 8 low Nef-dependent cell lines (MT4, HT1080, RAJI, DAUDI, C8166, IMR90, CEMX174 and WI38) were subjected to rRNA depletion using Ribo-Zero Magnetic Gold Kit (Epicentre). RNA-seq libraries were prepared from the rRNA depleted RNAs extracted from the 15 cell lines (Fig. 1a) using a modified protocol of the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2000 using paired-end sequencing 2?×?100?bp.  