|0.1 - 1 ug total RNA or 10 - 400 ng previously isolated mRNA (from species with polyA tails)
cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer’s instructions but without the polyA isolation stage. Of note, strand specificity is not achieved with this kit. Random hexamers were used for reverse transcription. Libraries were pooled and sequenced on an Illumina HiSeq 2500 system using the paired-end 50 mode.All reads were aligned to the human reference genome (hg19, GRCh37) using the bowtie 2 aligner with default parameters (only setting -N 1). We considered only reads mapped uniquely to the genome and not to chrUn_gl000220 (rRNA) for further analysis. For each experiment we constructed a genome-wide profile of the signal per disjoint 100 bp adjacent bins. The sum of each experiment was normalized to be 106. Full paper
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