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ChIP-seq of human embryonic stem cells (hESCs) overexpressed with Monkeypox viral proteins H3L and A29L

GSE239888 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 19 samples Submitted 2024/08/28 Platform GPL11154
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 19 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
19 samples: 6 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.
Paper
Monkeypox virus protein H3L induces injuries in human and mouseCell death & disease · 2024
Summary (written by the submitters)
We found that Monkeypox viral proteins H3L and A29L caused injuries in human cells. Whether they can bind chromatin and re-model chromation is unclear. Here, we applied ChIP-seq on hESCs to evaluate whether and how they are involved in chromatin regulation.
Published in
Monkeypox virus protein H3L induces injuries in human and mouse
Chen S, Huang G, Liu J · Cell death & disease 2024 · PMID 39168969 · doi:10.1038/s41419-024-06990-2
This dataset
Open GSE239888 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 GSE239888_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 PRJNA1001346 and SRA study SRP452971. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39168969) ↗
Study design
6 conditions, mostly in triplicate
H3L overexpression, anti-myc tag, ×3 H3L overexpression, anti-H3K4me3, ×3 H3L overexpression, anti-H3K27me3, ×3 A29L overexpression, anti-myc tag, ×3 A29L overexpression, anti-H3K4me3, ×3 A29L overexpression, anti-H3K27me3, ×3 1% Input ×1

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 19 sample titles; they account for 18 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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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.