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Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [ChIP-seq, Cut&Tag, ATAC-seq]

GSE253743 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 41 samples Submitted 2024/05/09 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 41 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
Homo sapiens (human)
Topic
Breast cancerThis series is part of our curated briefing on it.
Samples
41 samples: 12 conditions, mostly in duplicateGroups 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
Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancerNature cancer · 2024
Summary (written by the submitters)
To further elucidate the role of phospho-HDAC6 LLPS in transcriptional regulation, we performed RNA-seq experiments in TNBC cells treated with Nexturastat A or HDAC6 knockdown
Published in
Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer
Lu B, Qiu R, Wei J et al. · Nature cancer 2024 · PMID 39198689 · doi:10.1038/s43018-024-00816-y
This dataset
Open GSE253743 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Breast 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 GSE253743_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 PRJNA1066853 and SRA study SRP484763. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39198689) ↗
Study design
12 conditions, mostly in duplicate
MDA-MB231,Ctrl,ATAC, ×3 MDA-MB231,Nexturastat A,ATAC, ×3 MDA-MB231,shCtrl,ATAC, ×3 MDA-MB231,shHDAC6,ATAC, ×3 MDA-MB231,shHDAC6,HDAC6,Novus, ×2 MDA-MB231,Ctrl,HDAC6,cut&tag,Novus, ×2 MDA-MB231,Ctrl,Pan-acetyl,abcam, ×2 MDA-MB231,Nexturastat A,Pan-acetyl,abcam, ×2 +17 more

Supports a between-group comparison across 28 samples.

How we read this: 12 replicated groups read from 41 sample titles; they account for 28 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

+ 1 more — browse all 41 samples with per-sample file links →

More Breast cancer datasets

Search all human ChIP / ATAC / CUT&Tag 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.