Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable, BRAFV600E metastatic colorectal cancer [dataset 2]
RNA-seq (gene expression) · human · 12 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
- 12 samples
- 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.
Read the full summary ↓
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 GSE302922_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 PRJNA1292834 and SRA study SRP601646. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run VM1 … VM23 and carry no group information.
- GSM9113740 VM1
- GSM9113741 VM4
- GSM9113742 VM5
- GSM9113743 VM6
- GSM9113744 VM7
- GSM9113745 VM8
- GSM9113746 VM12
- GSM9113747 VM13
- GSM9113748 VM14
- GSM9113749 VM16
- GSM9113750 VM19
- GSM9113751 VM23
- 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
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing · shares metastatic
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE302921 Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable, BRAFV600E metastatic colorectal cancer [dataset 1] 50 samples shares brafv600e, microsatellite, encorafenib, metastatic, colorectal, cetuximab, nivolumab, stable
- GSE307398 Phase II Study of Pembrolizumab Plus Capecitabine and Bevacizumab for Microsatellite Stable/Mismatch Repair-Proficient Metastatic Colorectal Cancer 12 samples shares microsatellite, metastatic, colorectal, stable
- GSE319722 Spatial dynamics links PD-L1 and Tumor-Associated Macrophage–Enriched Niches to Immune and Mesenchymal States in microsatellite stable colorectal cancer 117 samples shares microsatellite, colorectal, stable
- GSE289582 Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab [Blood] 115 samples shares metastatic, colorectal, nivolumab
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.