Effect of FTO deletion on gene expression of HT29 and HCT116 in colon cancer cell lines
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: 3 × HT29 cell,WT, vs 3 × HT29 cell,FTOKO, vs 3 × HCT116 cell,WT, vs 3 × HCT116 cell,FTOKO,Groups 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
- FTO facilitates colorectal cancer chemoresistance via regulation of NUPR1-dependent iron homeostasisRedox biology · 2025
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 GSE278117_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 PRJNA1187843. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8540314 HT29 cell,WT,bio rep 1 HT29 cell,WT,
- GSM8540315 HT29 cell,WT,bio rep 2 HT29 cell,WT,
- GSM8540316 HT29 cell,WT,bio rep 3 HT29 cell,WT,
- GSM8540317 HT29 cell,FTOKO,bio rep 1 HT29 cell,FTOKO,
- GSM8540318 HT29 cell,FTOKO,bio rep 2 HT29 cell,FTOKO,
- GSM8540319 HT29 cell,FTOKO,bio rep 3 HT29 cell,FTOKO,
- GSM8540322 HCT116 cell,WT,bio rep 1 HCT116 cell,WT,
- GSM8540326 HCT116 cell,WT,bio rep 2 HCT116 cell,WT,
- GSM8540328 HCT116 cell,WT,bio rep 3 HCT116 cell,WT,
- GSM8540329 HCT116 cell,FTOKO,bio rep 1 HCT116 cell,FTOKO,
- GSM8540330 HCT116 cell,FTOKO,bio rep 2 HCT116 cell,FTOKO,
- GSM8540331 HCT116 cell,FTOKO,bio rep 3 HCT116 cell,FTOKO,
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing · shares colon
- 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
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE310036 Transcriptomic profiling of HCT116 and HT29 colorectal cancer cells after piR-37524 inhibition 12 samples shares hct116, ht29
- GSE276918 RNA decay profile for eRF1 and UPF1 depletion in HCT116 cell lines 48 samples shares hct116, lines
- GSE283223 RNA-seq analysis of melanoma cell lines with enhancer deletions. 39 samples shares deletion, lines
- GSE271991 Effect of red meat metabolites and nutrient deprivation on gene expression of HCT116 colorectal cancer cells 60 samples shares hct116
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.