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Sample GSM7159148 Query DataSets for GSM7159148
Status Public on Apr 29, 2024
Title 27_icaf
Sample type SRA
 
Source name cancer associated fibroblasts
Organism Mus musculus
Characteristics strain: FVB MMTV-PyMT
cell type: cancer associated fibroblasts
genotype: FVB MMTV-PyMT
treatment: No teatment
time: 10 weeks old
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Apr 10, 2023
Last update date Apr 29, 2024
Contact name Sheila Stewart
E-mail(s) sheila.stewart@wustl.edu
Organization name Washington University School of Medicine
Street address 660 South Euclid Avenue
City Saint Louis
ZIP/Postal code 314-362-7449
Country USA
 
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
Relations
SRA SRX19920658
BioSample SAMN34132752

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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