RNA sequencing of C57BL/6J mice, heterozygous for knockout of Hnrnph1 gene, as well as C57BL/6J mice controls

Previous studies of congenic lines of C57BL/6J-DBA/2J mice compared to C57BL/6 mice revealed a 0.23 QTL for sensitivity to methamphetamine on chromosome 11, which contains two protein coding genes, Rufy1 and Hnrnph1. Subsequent transcription activator-like effector nucleases (TALENs)-mediated introduction of frameshift deletions in the first coding exon of one copy of Hnrnph1 of C57BL/6J mice, revealed comparable association to phenotype. Analysis of the transcriptome and splicesome between these Hnrnph1 heterozygous knockouts and C57BL/6J mice revealed genome-wide differentially expression and exon usage of more than 1000 genes in either. Overall design: For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 C57BL/6J controls (B6) and 8 C57BL/6J Hnrnph1 heterozygous knockouts (H), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT (100bp paired-end reads). Samples 1-16, consisting of alternating experiments were run in four lanes total (each sample run on each lane) across 3 different flow cells. Raw samples provided are labeled with the "H1-" prefix, followed by the the sample number and the lane that it was run (L001, L002, or L008) and paired-end read number (R1 or R2). The tail of the file name pertains to the flow cell number (0009, 0012, or 0014).