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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 29, 2024 |
| Title |
27_vacf |
| Sample type |
SRA |
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| Source name |
cancer associated fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB MMTV-PyMT
cell type: cancer associated fibroblasts
genotype: FVB MMTV-PyMT
treatment: No teatment
time: 10 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were collected from 3 10-week-old FVB background MMTV-PyMT mice and then digested with 2 mg/mL Collagenase I and 2 U/mL Dnase. The cells were stained and suject to sorting to isolate each CAF population as described bellow. Sorted cells were directly collected into lyses buffer as instructed by Qiagen RNeasy Micro kit. RNA was further purified following the kit's protocol.
icaf: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C+; m2cafneg: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146-, PDGFRa+, NCAM-; m2cafpos: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146-, PDGFRa+, NCAM+; vCAF: icaf: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146+, PDGFRa-
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of gene and counts per million matrix including all samples
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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) |
| GSE229350 |
Senescent stroma mediates immunosuppression and drives breast cancer progression [CAF] |
| GSE229356 |
Senescent stroma mediates immunosuppression and drives breast cancer progression |
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| Relations |
| SRA |
SRX19920661 |
| BioSample |
SAMN34132749 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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