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| Status |
Public on Apr 29, 2024 |
| Title |
WT_CD45_neg |
| Sample type |
SRA |
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| Source name |
Mammary fat pad
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| Organism |
Mus musculus |
| Characteristics |
cell type: Non-immune cells
tissue: Mammary fat pad
strain: FVB MMTV-PyMT
age: 7 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
FVB background MMTV-PyMT+/INK-ATTAC- (WT) and MMTV-PyMT+/INK-ATTAC+ (INK+) mice were weaned and recruited to studies by 28-30 days of age. Administration of AP20187 (10 mg/kg, 3 doses/week) was delivered through intra peritoneal inections . By 7 weeks of age, tumor-bearing mammary fat pads were digested to single cell suspension, staied, and sorted into CD45+ and CD45- populations. Samples from 2 mice were pooled for each sample.
FVB background MMTV-PyMT+ mice were weaned and recruited to studies by 28-30 days of age. Administration of ABT737 (25 mg/kg/week) or vehicle (Veh) was delivered through intra peritoneal inections . By 7 weeks of age, tumor-bearing mammary fat pads were digested to single cell suspension, staied, and sorted into CD45+ and CD45- populations. Samples from 2 mice were pooled for each sample.
Immune cells: Live/DEAD- CD45+ cells were sorted; Non-immune cells: Live/DEAD- CD45- cells were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4/v5 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 10, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Sheila Stewart |
| E-mail(s) |
sheila.stewart@wustl.edu
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| Organization name |
Washington University School of Medicine
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| Street address |
660 South Euclid Avenue
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| City |
Saint Louis |
| ZIP/Postal code |
314-362-7449 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE229355 |
Senescent stroma mediates immunosuppression and drives breast cancer progression [scRNA-seq] |
| GSE229356 |
Senescent stroma mediates immunosuppression and drives breast cancer progression |
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| Relations |
| SRA |
SRX19922324 |
| BioSample |
SAMN34133103 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7159216_WT_CD45_neg_barcodes.tsv.gz |
22.0 Kb |
(ftp)(http) |
TSV |
| GSM7159216_WT_CD45_neg_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7159216_WT_CD45_neg_matrix.mtx.gz |
65.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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