3'-UTR-seq of Mus musculus female and male hypothalamus across the pubertal transition

The hypothalamus is a functionally and cellularly complex tissue controlling many developmental processes, including puberty. While key hormonal aspects of puberty regulation in the hypothalamus are well established, understanding the genes, cell-types, and epigenetic mechanisms underlying and regulating puberty is limited. Here, we performed 3'-UTR-seq on the hypothalamus from both sexes of C57BL/6J mice at 5 ages spanning pubertal transition (postnatal days 12, 22, 27, 32, 37) (4-5 replicates per sex at each age) to examine genome-wide age- and sex-biased trends in gene expression in a cell-type aware manner. Sample collection, RNA extraction, and sequencing was completed using the same protocols and on the same mice as PMID: 3622112 (E-MTAB-9459). QuantSeq 3' mRNA-seq libraries were constructed from total RNA using an automated method with Agilent NGS Workstation. The resulting single-end libraries were sequenced at SickKids TCAG core on the Illumina v4 flow cell with SR50 bp cycles extended to 68 bp. A customized pipeline was developed and used for the analysis of reads obtained (PMID: 36221127 for details). Processed reads were mapped to mouse genome (mm10).下丘脑是一类功能与细胞组成均极为复杂的组织，调控包括青春期发育在内的诸多生命进程。尽管目前对于下丘脑中青春期调控的关键激素环节已有较为充分的研究，但针对青春期发生与调控背后的基因、细胞类型及表观遗传机制的认知仍较为有限。本研究针对跨越青春期转变阶段的5个时间点（出生后第12、22、27、32、37天）的C57BL/6J小鼠（雌雄各半）的下丘脑组织开展3'非翻译区测序（3'-UTR-seq），每个年龄组的每个性别设置4-5个生物学重复，旨在以兼顾细胞类型特征的分析方式，解析全基因组范围内基因表达的年龄与性别偏倚趋势。本研究的样本采集、RNA提取与测序流程与PMID:3622112（E-MTAB-9459）所用方案完全一致，且实验动物为同一批小鼠。研究人员采用安捷伦NGS工作站（Agilent NGS Workstation）的自动化方法，从总RNA中构建QuantSeq 3' mRNA测序文库。所获得的单端测序文库于SickKids TCAG测序核心实验室，使用Illumina v4测序流动池（Illumina v4 flow cell）进行测序，测序循环为SR50 bp并延伸至68 bp。本研究开发了一套定制化分析流程用于所得测序reads的数据分析，相关细节可参考PMID:36221127。经预处理的测序reads被比对至小鼠参考基因组mm10。