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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
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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.
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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)
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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. |
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Submission date |
Oct 25, 2022 |
Last update date |
Sep 30, 2024 |
Contact name |
Olga Anczukow |
Organization name |
The Jackson Laboratory for Genomic Medicine
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Street address |
10 Discovery Drive
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City |
Farmington |
State/province |
CT |
ZIP/Postal code |
06032 |
Country |
USA |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (22)
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GSM6678930 |
OA20001, Mammary Glands Cells, rep4, 3months, scRNAseq |
GSM6678931 |
OA20002, Mammary Glands Cells, rep4, 18months, scRNAseq |
GSM6678932 |
OA20003, Mammary Glands Cells, rep5, 3months, scRNAseq |
GSM6678933 |
OA20004, Mammary Glands Cells, rep5, 18months, scRNAseq |
GSM6678934 |
OA20005, Mammary Glands Cells, rep6, 3months, scRNAseq |
GSM6678935 |
OA20006, Mammary Glands Cells, rep6, 18months, scRNAseq |
GSM6678936 |
OA20011, Mammary Glands Cells, rep1, 3months, scRNAseq |
GSM6678937 |
OA20013, Mammary Glands Cells, rep1, 18months, scRNAseq |
GSM6678938 |
OA20015, Mammary Glands Cells, rep2, 3months, scRNAseq |
GSM6678939 |
OA20017, Mammary Glands Cells, rep2, 18months, scRNAseq |
GSM6678940 |
OA20019, Mammary Glands Cells, rep3, 3months, scRNAseq |
GSM6678941 |
OA20021, Mammary Glands Cells, rep3, 18months, scRNAseq |
GSM6678942 |
OA20012, Mammary Glands Cells, rep1, 3months, snATACseq |
GSM6678943 |
OA20014, Mammary Glands Cells, rep1, 18months, snATACseq |
GSM6678944 |
OA20016, Mammary Glands Cells, rep2, 3months, snATACseq |
GSM6678945 |
OA20018, Mammary Glands Cells, rep2, 18months, snATACseq |
GSM6678946 |
OA20020, Mammary Glands Cells, rep3, 3months, snATACseq |
GSM6678947 |
OA20022, Mammary Glands Cells, rep3, 18months, snATACseq |
GSM7837730 |
Mammary Glands Cells, 18M, ST, Rep1 |
GSM7837731 |
Mammary Glands Cells, 18M, ST, Rep2 |
GSM8155366 |
Mammary Glands Cells, 3M, Rep1 |
GSM8155367 |
Mammary Glands Cells, 3M, Rep2 |
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Relations |
BioProject |
PRJNA894189 |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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