RNA was isolated using the miRNAEasy kit (Qiagen, 217004) according to the manufacturer’s instructions. All libraries were molecularly barcoded using TruSeq adaptors (Illumina) and sequenced on a HiSeq2000 (Illumina) using paired-end 75 cycle reads. The assembly of transcripts estimation of their abundances, and tests for differential expression were performed using Tophat (transcriptome version: Ensembl Homo_sapiens.GRCh37.73.gtf) and Cufflinks-Cuffdiff v1.040 (transcriptome version: Illumina's igenomes Ensembl GRCh37). To increase statistical power, FPKM values were averaged from both parental control CXCR4+ NPC samples and both replicates of the BD-patient CXCR4+ NPCs GM05224. Only transcripts with sufficient read depth in both conditions as determined by Cuffdiff analysis were considered in subsequent analysis.
