Queryable single-cell RNA-seq (10x Genomics) datasets of Human and Mouse spermatogenic cells

Published: 07-11-2018| Version 1 | DOI: 10.17632/kxd5f8vpt4.1
Contributor:
Brian Hermann

Description

To reveal distinct transcriptomes associated with various spermatogenic cells in both mouse and human testes, including spermatogonial stem cells (SSCs) and all of their subsequent progeny, we used the 10x Genomics Chromium (a commercialized Drop-Seq variant) to perform single-cell RNA-seq on various cell populations. Raw data and analyzed data (gene expression matrices) are deposited into the NIH GEO database. Here we include queryable, annotated and interactive files that can be used to compare single-cell transcriptomes. Spermatogonia from immature (P6) and adult Id4-Egfp transgenic mice were used. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. Corresponding human spermatogonia were enriched from human testicular tissue by multi-parameter FACS. For both human and mouse, StaPut gravity sedimentation enriched for meiotic spermatocytes and post-meiotic spermatids and we profiled unselected steady-state spermatogenic cells. The data from these experiments are stored in Loupe Cell Browser files (.cloupe) which are generated during analysis of 10x Genomics Single-cell data and can be opened and queried with the Loupe Cell Browser (10X Genomics). This software can be downloaded for free from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. It is important to note that the companion manuscript for these data used additional analyses that are not represented in these files. The following datasets are available: 1. Unselected or sorted P6 ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim) were used for this study. Data are from 13094 cells and can be found in the following file: P6 Mouse Spermatogonia.cloupe (aggregate of three datasets, P6 ID4-EGFP bright/dim/unselected) 2. Unselected or sorted Adult ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim), three replicate preparations of steady-state unselected spermatogenic cells, and StaPut-enriched adult spermatocytes and spermatids were used for this study. Data are from 17491 cells and can be found in the following files: Adult Mouse Sorted Spermatogonia.cloupe (Aggregated Ad Spg- ID4-EGFP bright/dim/CD9bright) Mouse Unselected Spermatogenic cells.cloupe (3 replicates of steady-state spermatogenic cells) Mouse StaPut Spermatocytes.cloupe Mouse StaPut Spermatids.cloupe 3. Sorted adult Human spermatogonia, three replicates of steady-state unselected spermatogenic cells, and StaPut-enriched adult spermatocytes and spermatids were used. Data are from 32727 cells and can be found in the following files: Human Sorted Spermatogonia.cloupe (3 replicates) Human Unselected Spermatogenic Cells.cloupe (3 replicates of steady-state spermatogenic cells) Human StaPut Spermatocytes.cloupe (2 replicates) Human StaPut Spermatids.cloupe (2 replicates)

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