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A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma

GSE213360 Danio rerio (zebrafish) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2024/06/13 Platform GPL21741Platform GPL20301Platform GPL20828
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · zebrafish · 40 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
Danio rerio (zebrafish)
Topic
MelanomaThis series is part of our curated briefing on it.
Samples
40 samples: 7 conditions, mostly in triplicateGroups 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.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE213360 in finder → Find more ChIP / ATAC / CUT&Tag datasets → Melanoma 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 GSE213360_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA880593 and SRA study SRP397063. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly in triplicate
Vehicle Control treated A375 ×3 10ng/mL TGFB1 treated A375 ×3 Vehicle Control treated ZMEL1 ×3 10ng/mL TGFB1 treated ZMEL1 ×3 EGFP MCR:MCS Tumor 1 GFP+ # ×3 EGFP MCR:SATB2 Tumor 1 GFP+ # ×3 EGFP MCR:MCS Tumor 2 GFP+ # ×3 Vehicle Control A375 INPUT 6.11 ×1 +18 more

Supports a case/control comparison: 26 samples read as cases, 8 as controls.

How we read this: 7 replicated groups read from 40 sample titles; they account for 21 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 Melanoma datasets

Search all ChIP / ATAC / CUT&Tag 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.