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Class I histone deacetylases HDAC1, 2 and 3 are histone decrotonylases

GSE96035 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 33 samples Submitted 2017/12/16 Platform GPL17021Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 33 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)
Samples
33 samples: 10 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.
Summary (written by the submitters)
We characterize histone crotonylation in intestinal epithelium-derived cells through Mass spectrometry, ChIp-Seq and RNA-Seq approaches and show that this modification is removed by class I histone deacetylases, HDAC1, 2 and 3.
This dataset
Open GSE96035 in finder → Find more RNA-seq datasets →
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 GSE96035_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 PRJNA378641 and SRA study SRP101638. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29317660) ↗
Study design
10 conditions, mostly in triplicate
RNAseq_HCT116.DMSO ×4 RNAseq_HCT116.MS275 ×4 RNAseq_colonepithelium ×3 H3K4me3ChIP_colonepithelium_ChIP ×3 H3K18acChIP_HCT116_ChIPDMSO ×3 H3K18acChIP_HCT116_ChIPMS275 ×3 H3K18crChIP_HCT116_ChIPDMSO ×3 H3K18crChIP_HCT116_ChIPMS275 ×3 +5 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 33 sample titles; they account for 30 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
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