Illumina HiSeq 2500 paired end sequencing
RNA-Seq from isolated CD48+ LSK cells which resided in a mutant (loss of the gene SBDS) bone marrow environment
cDNA was synthesized and amplified using SMARTer Ultra Low RNA kit (Clontech Laboratories) following the manufacturer’s protocol. Amplified cDNA was further processed according to TruSeq Sample Preparation v.2 Guide (Illumina) and paired-end sequenced (2x75 bp) on the HiSeq 2500 (Illumina). Demultiplexing was performed using CASAVA software (Illumina) and the adaptor sequences were trimmed with Cutadapt (http://code.google.com/p/cutadapt/).