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Series GSE216542 Query DataSets for GSE216542
Status Public on Sep 29, 2024
Title scRNA-seq, snATAC-seq, and spatial transcriptomics analysis of mammary glands of aged female mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Aging results in changes in mammary gland cell proportions, gene expression, and chromatin accessibility. Cell types captured include epithelial, immune, and stromal cell types.
 
Overall design Mammary gland 3M and 18M old virgin female C57BL/6J mice were enzymatically and mechanically digested. Single cells were FACS-sorted based on viability prior to performing scRNA-seq (10X Chromium v.3 chemistry) and snATAC-seq (10X Chromium v.1)
 
Contributor(s) Angarola B, Katiyar N, Sharma S, Kang HG, Nehar-Belaid D, Anczukow O, Ucar D
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 25, 2022
Last update date Sep 30, 2024
Contact name Olga Anczukow
Organization name The Jackson Laboratory for Genomic Medicine
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (22)
GSM6678930 OA20001, Mammary Glands Cells, rep4, 3months, scRNAseq
GSM6678931 OA20002, Mammary Glands Cells, rep4, 18months, scRNAseq
GSM6678932 OA20003, Mammary Glands Cells, rep5, 3months, scRNAseq
Relations
BioProject PRJNA894189

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
GSE216542_ATAC_Counts_Final.rds.gz 470.4 Mb (ftp)(http) RDS
GSE216542_ATAC_Metadata_Final.txt.gz 3.1 Mb (ftp)(http) TXT
GSE216542_RAW.tar 285.0 Mb (http)(custom) TAR (of CSV, JPG, JSON, MTX, PNG, TIFF, TSV)
GSE216542_RNA_Counts_Final.rds.gz 233.1 Mb (ftp)(http) RDS
GSE216542_RNA_Metadata_Final.txt.gz 1.4 Mb (ftp)(http) TXT
GSE216542_ST.xlsx 128.4 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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