| Experiment Id | GSE76929 | Name | RNA sequencing of C57BL/6J mice, heterozygous for knockout of Hnrnph1 gene, as well as C57BL/6J mice controls |
| Experiment Type | RNA-Seq | Study Type | WT vs. Mutant |
| Source | GEO | Curation Date | 2023-10-10 |
| description | 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. 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). |
