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Heritable human Polycomb silencing is locus-dependent and requires H2AK119ub1 self-propagation

GSE209986 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2024/05/15 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 48 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
48 samples: 21 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
Genomic context- and H2AK119 ubiquitination-dependent inheritance of human Polycomb silencingScience advances · 2024
Summary (written by the submitters)
Heritable gene silencing is essential for the development of multicellular organisms. Polycomb repressive complexes 1 and 2 (PRC1 and 2) catalyze and recognize histone H2A lysine 119 mono-ubiquitination (H2AK119ub1) and histone H3 lysine 27 trimethylation (H3K27me3), respectively, to mediate heritable gene silencing, but the mechanism of inheritance is not fully understood.
Read the full summary ↓
Using an inducible gene silencing strategy, we show that the epigenetic inheritance of Polycomb silencing in human cells is strongly dependent on local DNA sequences and chromatin environment. In addition, we find that inheritance is not strictly dependent on H3K27me3 recognition and can be partially achieved by H2AK119ub1 catalysis and recognition, independently of H3K27me3. These findings demonstrate that locus specific features and H2AK119ub1 play key roles in inheritance of Polycomb silencing in human cells.
Published in
Genomic context- and H2AK119 ubiquitination-dependent inheritance of human Polycomb silencing
Shafiq TA, Yu J, Feng W et al. · Science advances 2024 · PMID 38718120 · doi:10.1126/sciadv.adl4529
This dataset
Open GSE209986 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 GSE209986_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 PRJNA863276. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38718120) ↗
Study design
21 conditions, mostly in duplicate
WT1,RING1ABKO,DoxycyclineAddition, H3K27me3, ×3 WT1,RING1ABKO,DoxycyclineRemoval, H3K27me3, ×3 WT1, NoDoxycycline, H3K27me3, ×2 WT1,DoxycyclineAddition, H3K27me3, ×2 WT1,DoxycyclineRemoval, H3K27me3, ×2 WT1,EEDKO,DoxycyclineAddition, H3K27me3, ×2 WT1,EEDKO,DoxycyclineRemoval, H3K27me3, ×2 WT1,HAEED,DoxycyclineAddition, H3K27me3, ×2 +17 more

Supports a between-group comparison across 44 samples.

How we read this: 21 replicated groups read from 48 sample titles; they account for 44 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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