RNA-seq 6 day timecourse for K562 cells grown in hypoxia/normoxia (21%, 5%, 1% oxygen)

K562 cells were grown at different oxygen levels (21%, 5%, 1%) and samples were collected at 6hr, 24hr, 3day, and 6day time points (triplicate per time point). Overall design: RNA-seq was performed for K562 cells grown in 3 oxygen levels (21%, 5%, 1%) at 4 time points (6hr, 24hr, 3day, 6day) for each of 3 replicates. K562 cells were seeded at a density of 1e5/ml in 3ml of DMEM media per well of 6-well plate. Plates were maintained in 1%, 5% or 21% O2 incubators and passaged at 3d of growth. At each time point, cells were pelleted, rinsed with PBS and then stored at -80C. RNA extraction was performed using the Qiagen RNAeasy kit. The RNASeq libraries were generated as described (Picelli et al., 2014; Trapnell et al., 2012). RNA was isolated using RNASPRI beads. Following reverse transcription, cDNA was fragmented and barcoded. Samples were subjected to paired-end sequencing of 2x25bp. RNASeq data was processed using the Cufflinks suite (tophat, cuffquant, cuffnorm) as previously described (Trapnell et al., 2012).