← BioTransfer GEO Dataset Finder
GEO series

THE INTEGRATIVE GENOMIC AND FUNCTIONAL IMMUNOLOGICAL ANALYSES OF COLORECTAL CANCER INITIATING CELLS TO MODULATE STEMNESS PROPERTIES AND THE SUSCEPTIBILIY TO IMMUNE RESPONSES [RNA-Seq]

GSE287597 Homo sapiens (human) RNA-seq (gene expression) 55 samples Submitted 2025/02/26 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 55 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
55 samples: 49 distinct titles, 6 of them repeatedGroups 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.
Paper
The integrative genomic and functional immunological analyses of colorectal cancer initiating cells to modulate stemness properties and the susceptibility to immune responsesJournal of translational medicine · 2025
Summary (written by the submitters)
We conducted a the transcriptomic profile of CICs or FBS cell lines, upon treatment or not with immunomodulatory or epigenetic drugs or with miRNA modulators, using the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen). Differentially expressed genes (DEGs) were assessed in CICs and FBS cell line pairs (#1076 and 1247) upon treatment with either miRNA-15a or -196a modulators (inhibitors or mimics) or immunomodulatory or epigenetic agents (HDACi, butyrate or IFN-γ + butyrate).
Read the full summary ↓
Numerous DEGs were detected among the comparisons of the different treatments. In CICs, N= 176, 238, 131, 168, 1155, 1237 and 1368 DEGs were significantly (p<0.05) detected following their treatment with miR-15a mimic or inhibitor, miR-196a mimic or inhibitor, butyrate, HDACi or IFN-γ + butyrate, respectively. The results corroborated the role of miRNA-15a and miRNA-196a mimics and of epigenetic drugs as beneficial treatments to improve CRC-specific immune responses through mechanisms including TGF-β signaling downmodulation, HLA and APM upregulation and negative regulation of tumorigenic pathways.
Published in
The integrative genomic and functional immunological analyses of colorectal cancer initiating cells to modulate stemness properties and the susceptibility to immune responses
Tout I, Bougarn S, Toufiq M et al. · Journal of translational medicine 2025 · PMID 39962504 · doi:10.1186/s12967-025-06176-0
This dataset
Open GSE287597 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 GSE287597_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 PRJNA1213794 and SRA study SRP558743. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39962504) ↗
Study design
49 distinct titles, 6 of them repeated
1247CSCUT ×2 1247FBSUT ×2 1247CSCmiR-196amimic ×2 1247FBSmiR-196amimic ×2 1076CSCmiR-196amimic ×2 1076FBSmiR-196amimic ×2

How we read this: Read from 55 sample titles: 49 distinct titles with little repetition. 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

+ 15 more — browse all 55 samples with per-sample file links →

More Colorectal cancer datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

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.