Ceramides drive colorectal cancer metastasis through a revival stemness program [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × organoid, HFD, vs 3 × organoid, CD, vs 3 × organoid, Control, vs 3 × organoid, PA-treated,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.
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 GSE285872_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1206687 and SRA study SRP555350. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 3 as controls.
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.
- GSM8711785 organoid, HFD, rep1 organoid, HFD,
- GSM8711786 organoid, HFD, rep2 organoid, HFD,
- GSM8711787 organoid, HFD, rep3 organoid, HFD,
- GSM8711788 organoid, CD, rep1 organoid, CD,
- GSM8711789 organoid, CD, rep2 organoid, CD,
- GSM8711790 organoid, CD, rep3 organoid, CD,
- GSM8711791 organoid, Control, rep1 organoid, Control,
- GSM8711792 organoid, Control, rep2 organoid, Control,
- GSM8711793 organoid, Control, rep3 organoid, Control,
- GSM8711794 organoid, PA-treated, rep1 organoid, PA-treated,
- GSM8711795 organoid, PA-treated, rep2 organoid, PA-treated,
- GSM8711796 organoid, PA-treated, rep3 organoid, PA-treated,
- GSE286166 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_CRISPR] 34 samples shares colorectal, metastasis, ceramides, stemness, revival, program, drive
- GSE286167 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_HFD] 23 samples shares colorectal, metastasis, ceramides, stemness, revival, program, drive
- GSE285873 Ceramides drive colorectal cancer metastasis through a revival stemness program [scRNA-seq] 10 samples shares colorectal, metastasis, ceramides, stemness, revival, program, drive
- GSE290751 Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis [ATAC-seq_met] 15 samples shares colorectal, metastasis, atac-seq, drive
- GSE256013 TGF-β and RAS jointly unmask primed enhancers to drive metastasis (ATAC-Seq) 12 samples shares metastasis, atac-seq, drive
- GSE326232 Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis [H3K27ac_CUT&RUN] 8 samples shares colorectal, metastasis, drive
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares colorectal, program, drive
- GSE290756 Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis 50 samples shares colorectal, metastasis, drive
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.