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SRX14633680: GSM5974486: TNBC1; Homo sapiens; RNA-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 304.3M spots, 40.2G bases, 16.9Gb downloads

External Id: GSM5974486_r1
Submitted by: Cancer Center, Stony Brook University
Study: Comparative single-cell genomics uncovers evolutionarily conserved features and therapeutic targets in triple-negative breast cancer fibroblasts
show Abstracthide Abstract
We performed scRNA-seq analysis of fibroblasts from murine and human TNBCs. We observed three CAF subtypes in mouse TNBC: two transcriptionally distinct CAFs that were found intermingled and adjacent to tumor cells, and distal CAFs that were located further away from tumor cells. All three CAFs appear to evolve from normal resident fibroblasts/pericytes by activation of Pdgf and Tgfb receptors in fibroblasts in parallel with reciprocal upregulation of ligands in tumor cells and other tumor microenvironment cells. Additionally, extracellular matrix, glycolytic and mitochondrial respiratory genes were strongly upregulated in all three CAFs. Murine pancreatic CAFs displayed matching subtypes. Human TNBCs displayed three analogous CAF subtypes, although only a subset of marker genes are conserved. Finally, the upregulation of specific extracellular matrix genes in different CAF subtypes provides a basis for developing selective CAF-targeted therapeutics. Overall design: scRNAseq was performed on a total of thirteen samples: three human samples and ten mouse samples. The human tissue samples of triple negative breast tumors were provided by the NCI Cooperative Human Tissue Network. The murine breast tumor samples were harvested from mammary glands of two transgenic mouse models: a) MMTV-PyMT and b) C3(1)-Tag SV40. The pancreatic tumor came from the Ptf1?-CreERTM; LSL- KRASG12D strain. .
Sample: TNBC1
SAMN27018998 • SRS12400020 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM5974486
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform. Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.
Runs: 2 runs, 304.3M spots, 40.2G bases, 16.9Gb
Run# of Spots# of BasesSizePublished
SRR18502269123,999,25516.4G6.9Gb2022-09-01
SRR18502270180,272,11323.8G10Gb2022-09-01

ID:
20935986

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