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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (ChIP-Seq)

GSE232112 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 17 samples Submitted 2024/10/15 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 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
17 samples: 8 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
Control of Intestinal Stemness and Cell Lineage by Histone Variant H2A.Z IsoformsMolecular and cellular biology · 2024
Summary (written by the submitters)
The involvement of the histone variant H2A.Z and its isoforms in the regulation of gene expression is an increasing exciting field considering the impact of such regulations in physio-pathology. Indeed, we and other recently showed that H2A.Z.1 and H2A.Z.2 isoforms exert cooperative or antagonistic transcriptional regulations on subsets of genes involved in key processes, such as proliferation, senescence or several organ functions.
Read the full summary ↓
In this work, we analyze the relative role of both H2A.Z isoforms on parameters of the intestinal epithelial homeostasis. We observed that the amount of H2A.Z.1 and H2A.Z.2 at TSS and gene bodies are highly correlated and that the two H2A.Z isoforms can replace each other when depleted. We highlighted the role of their respective deposition onto chromatin by specific incorporators in some discrete isoform-specific contribution to the differentiation process. We have also uncovered an unexpected link between H2A.Z isoforms occupancy at gene bodies and the propensity of genes to be induced in enterocyte differentiation.
Published in
Control of Intestinal Stemness and Cell Lineage by Histone Variant H2A.Z Isoforms
Rispal J, Rives C, Jouffret V et al. · Molecular and cellular biology 2024 · PMID 39155414 · doi:10.1080/10985549.2024.2387720
This dataset
Open GSE232112 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE232112_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 PRJNA970836 and SRA study SRP436713. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39155414) ↗
Study design
8 conditions, mostly in duplicate
Caco-2/15-Z1flag Postconfluent cells IP Flag … ×2 Caco-2/15-Z1flag Postconfluent cells IP H2A.Z… ×2 Caco-2/15-Z1flag Subconfluent cells IP Flag E… ×2 Caco-2/15-Z1flag Subconfluent cells IP H2A.Z … ×2 Caco-2/15-Z2flag Postconfluent cells IP Flag … ×2 Caco-2/15-Z2flag Postconfluent cells IP H2A.Z… ×2 Caco-2/15-Z2flag Subconfluent cells IP Flag E… ×2 Caco-2/15-Z2flag Subconfluent cells IP H2A.Z … ×2 +1 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 17 sample titles; they account for 16 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
Datasets on a similar topic

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