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Series GSE145443 Query DataSets for GSE145443
Status Public on Feb 19, 2020
Title An atlas of cell types in the mammalian epididymis and vas deferens [single-cell RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The epididymis is comprised of multiple segments/compartments that, in addition to concentrating sperm and preventing their premature activation, play key roles in remodeling the protein, lipid, and RNA composition of maturing sperm. In order to understand the complex roles for the epididymis in reproductive biology, we generated a single cell atlas of gene expression from the murine epididymis and vas deferens using droplet-based (10X Chromium) single cell RNA-Seq. Following single-cell RNA-Seq, quality control, and removal of reads attributable to contaminating cell-free RNA we were able to profiled the expression of 16878 genes in 8,880 individual cells with an average of 3110 (median = 1965) unique molecular identifiers (UMIs) per cell from across the epididymis and the vas deferens. We recovered all the key cell types of the epididymal epithelium, including principal cells, clear cells, and basal cells, along with its associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Our data confirm and extend prior studies of segment-restricted gene expression programs, and reveal that these region-specific programs are largely driven by principal cells. In addition to the extensive region-specific specialization of principal cells, we find evidence for functionally-specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Furthermore, we find several novel cell subpopulations, most notably including an Amylin-positive clear cell subtype, and predict intercellular signaling networks between the various cell types. Together, these data provide an atlas of cell composition across the epididymis, and a wealth of molecular hypotheses for future efforts in reproductive physiology.
 
Overall design Sperm-depleted single cell suspensions were obtained from eight epididymides from four 10-12 weeks old FVB mice. The organ was cut into four segments that roughly corresponded to caput, corpus, cauda, and vas deferens. Single-cell RNA sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics).
 
Contributor(s) Rinaldi V, Donnard E, Rando O
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Submission date Feb 18, 2020
Last update date Feb 19, 2020
Contact name Elisa Donnard
Organization name University of Massachusetts Medical School
Department Bioinformatics and Integrative Biology
Lab Garber
Street address 368 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM4318432 Caput
GSM4318433 Cauda
GSM4318434 Corpus
Relations
BioProject PRJNA607227
SRA SRP249803

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE145443_metadata_SC_epid.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE145443_raw_SC_epid.tsv.gz 12.4 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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