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RNA-seq between between FOLFOX chemotherapy sensitivity and insensitivity in colorectal cancer

GSE200407 Homo sapiens (human) RNA-seq (gene expression) 22 samples Submitted 2025/04/07 Platform GPL17303
At a glance

RNA-seq (gene expression) · human · 22 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
22 samples: 13 × Colorectal cancer tissue, Insensitive vs 9 × Colorectal cancer tissue, SensitiveGroups 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.
Summary (written by the submitters)
22 cases of advanced stage CRC who had received preoperative neoadjuvant mFOLFOX before radical resection. All enrolled cases were adult patients with cytologically or histologically confirmed colorectal adenocarcinoma by at least two pathologists and with no history of any neoadjuvant anti-tumor therapy. All patients received 2-4 courses of preoperative neoadjuvant mFOLFOX before surgery, after which patients were organized into 2 groups according to TRG.
Read the full summary ↓
9 cases (<2 TRG scores) were included in mFOLFOX sensitive group, while the other 13 cases (2~3 TRG scores) were included in mFOLFOX insensitive group.
This dataset
Open GSE200407 in finder → Find more human RNA-seq datasets → Colorectal cancer landscape →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE200407_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA824463 and SRA study SRP368043. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
13 × Colorectal cancer tissue, Insensitive vs 9 × Colorectal cancer tissue, Sensitive

Supports a between-group comparison across 22 samples.

How we read this: 2 replicated groups read from 22 sample titles; they account for 22 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.

Samples in this study
More Colorectal cancer datasets

Search all human RNA-seq datasets in GEO →

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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.