title: RNA-Seq of HEK293T: transfected with siLuc
design: RNA isolation was done using the miRNeasy minikit (Qiagen). The RNA 6000 Nano kit (Agilent technologies) was used to confirm RNA integrity before the RNA was subjected to poly(A) enrichment. cDNA synthesis, library preparation and sequencing were carried out using the Ion Total RNA-Seq kit v2, the Ion PI Template OT2 200 kit v3 and the Ion Sequencing 200 kit v3, respectively, according to the manufacturers instructions (Invitrogen). RNA was sequenced on an Ion Proton System at a depth of approximately 20 million reads per sample, with a median read length of 90bp. Sequence files obtained in the bam format were converted to fastq using the bam2fastq conversion utility from the bedtools package. Reads were aligned to the human genome build GRCh37  Ensembl using Tophat2 (version 2.0.10). In a second alignment step, Bowtie2 (version 2-2.10) was used in the local, very sensitive mode to align remaining un-aligned reads. HTSeq-Coumt (version 0.6.1) was used with default settings to quantify gene expression. Finally, DESeq (version 1.2.10) was used to generate a list of genes differentially expressed between CHD7-depleted and control cells.