title: Illumina HiSeq 2000 paired end sequencing
design: RNA was extracted from EndoC-βH1 and EndoC-βH2 cell lines using TRIzol and sequenced at the Oxford Genomics Centre (Wellcome Trust Centre for Human Genetics, University of Oxford). After poly-A selection, strand-specific libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Libraries were sequenced to a total depth of ~50 million read pairs as a multiplex with other samples over two lanes of  Illumina  HiSeq2000  as  100-nucleotide  paired-end  reads using  the Illumina TruSeq  PE  Cluster  Generation  and  TruSeq  SBS  v3 kits.  STAR version 2.5.1b on  was  used  to  align  sequencing  reads  to  the  human genome reference GRCh37.p13, and using GENCODE release 19 as the transcriptome reference.  Gene counts were quantified using featureCounts v1.5.0-p2, and converted into TPM (Transcripts Per kilobase Million).