Cancer-Associated Fibroblasts Promote Vasculogenic Mimicry of Colorectal Cancer by Epigenetic Silencing of Decorin [RNA-Seq]
RNA-seq (gene expression) · human · 24 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 24 samples: 12 × NF vs 12 × CAFGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE271350_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1130974 and SRA study SRP517603. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 2 replicated groups read from 24 sample titles; they account for 24 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8375134 NF1 NF
- GSM8375135 NF2 NF
- GSM8375136 NF3 NF
- GSM8375137 NF4 NF
- GSM8375138 NF5 NF
- GSM8375139 NF6 NF
- GSM8375140 NF7 NF
- GSM8375141 NF8 NF
- GSM8375142 NF9 NF
- GSM8375143 NF10 NF
- GSM8375144 NF11 NF
- GSM8375145 NF12 NF
- GSM8375146 CAF1 CAF
- GSM8375147 CAF2 CAF
- GSM8375148 CAF3 CAF
- GSM8375149 CAF4 CAF
- GSM8375150 CAF5 CAF
- GSM8375151 CAF6 CAF
- GSM8375152 CAF7 CAF
- GSM8375153 CAF8 CAF
- GSM8375154 CAF9 CAF
- GSM8375155 CAF10 CAF
- GSM8375156 CAF11 CAF
- GSM8375157 CAF12 CAF
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE335811 Macrophage-Induced Senescent Cancer-Associated Fibroblasts Promote SASP-Mediated Chemoresistance in Colorectal Cancer 12 samples shares cancer-associated, fibroblasts, colorectal, promote
- GSE309392 Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [scRNA-Seq] 23 samples shares cancer-associated, fibroblasts, promote
- GSE314456 Adipose stromal cell-derived cancer-associated fibroblasts promote pancreatic adenocarcinoma through SFRP4 signaling 20 samples shares cancer-associated, fibroblasts, promote
- GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 samples shares cancer-associated, fibroblasts
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.