Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice
Creators: name: Sokolowski, Dustin
name: Hou, Huayun
name: E. Yuki, Kyoko
name: Roy, Anna
name: Chan, Cadia
name: Choi, Wendy W.Y.
name: Faykoo-Martinez, Mariela
name: Hudson, Matt
name: Corre, Christina
name: Uuskula-Reimand, Liis
name: Goldenberg, Anna
name: Palmert, Mark R.
name: Wilson, Michael D.
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310505
subject: Gene expression (incl. microarray and other genome-wide approaches)
classificationCode: 310903
subject: Animal developmental and reproductive biology

description: This figshare contains the scripts and data required to reproduce the figures generated in Sokolowski et al., Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice <br>Preprint: https://www.biorxiv.org/content/10.1101/2023.10.12.562121v1<br>Abstract: Although the hypothalamus plays a critical role in the regulation of puberty, more research is needed to identify the gene regulatory networks that control pubertal timing. Here, we investigate the age-, sex- and cell-type-specific gene regulation in the hypothalamus across the pubertal transition. We used RNA-seq to profile hypothalamic gene expression in male and female mice at five time points spanning the onset of puberty (postnatal days (PD) 12, 22, 27, 32, and 37). By combining this data with hypothalamic scRNA-seq data of pre- and post-pubertal mice, we were able to assign gene expression changes to their cell types of origin. In our colony, pubertal onset occurs earlier in male mice allowing us to focus on genes whose expression is dynamic across ages and offset between sexes and to explore bases of sex effects. Our age-by- sex pattern of expression enriched for biological pathways involved hormone production, neuronal activation, and glial maturation. Additionally, we found a dramatic expansion of oligodendrocytes precursor cells into mature oligodendrocytes spanning the pre-pubertal (PD12) to peri-pubertal (PD27) timepoints, and that genes driving this expansion enrich for genes involved in pubertal regulation. Together, by incorporating multiple biological timepoints with male and female mice simultaneously, our work furthers the understanding of gene and cell-type changes that accompany the development of secondary sex characteristics in both sexes.<br>Data repository (ArrayExpress): E-MTAB-12340<br>Corresponding Author:- Michael Wilson. Michael-dot-wilson-at-sickkids-dot-caWriter of FigShare: - Dustin Sokolowski. djsokolowski95-at-gmail-dot-com<br>It's likely that I will have an easier tracking down files that you may need, so please include both of us in youremail if you need data in your correspondence.<br>For example, to keep the repository at a reasonable size, we removed intermediate and final-processed files greater than 100Mb in size. - these data files can all be reproduced using the scripts in the directory.<br>There are four main sections of the repo:shiny_bundle is a downloaded version of our shiny app. https://wilsonlab-sickkids-uoft.shinyapps.io/hypothalamus_gene_shiny/- This app should be able to be loaded into R and run as a local instance <br>sh: the bash scripts used in read trimming, alignment, and quantification. - aside from the custom trimming of polyT primers, the alignment and counting used STAR, samtools, picard, and featurecounts - using standard parameters data: a directory with the starting, intermediate, and (size permitting) processed files used in this paper- rather than data being split by each figure, the data is split by each major analysis.<br>Manuscript_code: All of the R scripts we used to generate the main and supplementary figures of this studyWhile the scripts should run with the below packages installed, not all scripts have their directories such thateach file works instide /Manuscript_code and is associated with /Manuscript_code/data. If there are issues with finding files,it is likely a pathing issue rather than missing data. If data is however missing then please reach out.<br>The following R packages are used in this figshare:<br># Plottinglibrary(ggplot2)library(ggfortify)library(dplyr)library(tidyr)library(UpSetR)library(ComplexHeatmap)library(reshape2)library(ggpubr)library(ggrepel)library(pheatmap)library(grDevices)library(RColorBrewer)<br>#enrichment<br>library(ActivePathways)library(gProfileR)require(scales)library(DEET)library(gprofiler2)<br># single-cell RNA-seq processing and analysis (exlcuding RNA-seq deconvolution)<br>library(Seurat)library(sctransform)library(slingshot)library(optparse)library(tradeSeq)library(clusterExperiment)library(scater)library(MAST)library(patchwork) # for spatial analysis<br><br># Bulk RNA-seq analysis<br>library(RUVSeq)library(edgeR)library(DESeq2)<br># Bulk and scRNAseq analysislibrary(BiocParallel)library(scran) # nopelibrary(gplots)library(NMF)library(scMappR)library(BayesPrism)<br>--- R packages for comparing decvonvolution tools (includes duplicate packages):library(scBio)library(BisqueRNA)library(Seurat)library(MuSiC)library(SummarizedExperiment)library(xbioc) # Required for MuSiClibrary(dplyr)library(reshape)library(wgcna)library(cpm)<br>--- Writing tableslibrary(xlsx)