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. 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).既往针对C57BL/6J-DBA/2J同源导入近交系小鼠（相较于C57BL/6小鼠）的研究显示，其11号染色体上存在一个效应值为0.23的、与甲基苯丙胺敏感性相关的数量性状位点（Quantitative Trait Locus, QTL），该位点包含两个蛋白编码基因：Rufy1与Hnrnph1。后续研究通过转录激活因子样效应物核酸酶（Transcription Activator-Like Effector Nucleases, TALEN）介导，在C57BL/6J小鼠Hnrnph1基因单拷贝的首个编码外显子中引入移码缺失突变，所得模型表现出与该表型一致的关联特征。对该Hnrnph1杂合敲除小鼠与野生型C57BL/6J小鼠的转录组及剪接体进行分析后发现，两组小鼠体内均有超过1000个基因发生全基因组范围的差异表达与外显子使用模式改变。本研究收集了16只小鼠的双侧纹状体半球的3mm直径组织打孔样本，并将同组样本混合：其中8只为C57BL/6J对照组（记为B6），另外8只为C57BL/6J Hnrnph1杂合敲除组（记为H）；随后提取总RNA，采用Illumina TruSeq Stranded mRNA LT试剂盒进行cDNA文库构建，采用100bp双端测序读段进行测序。样本1至16采用交替实验设计，共分配至4个测序泳道（每个样本在每个泳道均完成测序），并横跨3个不同的测序流动池。本次提供的原始测序样本以"H1-"作为前缀标识，其后依次为样本编号、对应测序泳道编号（L001、L002或L008）以及双端读段编号（R1或R2）；文件名后缀则对应测序流动池编号（0009、0012或0014）。