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UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation

GSE256033 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 79 samples Submitted 2024/10/23 Platform GPL21145Platform GPL24676Platform GPL20795
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 79 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
79 samples: 53 distinct titles, 13 of them repeatedGroups 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
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylationNucleic acids research · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation
Tiedemann RL, Hrit J, Du Q et al. · Nucleic acids research 2024 · PMID 39607687 · doi:10.1093/nar/gkae1105
This dataset
Open GSE256033 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 GSE256033_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 PRJNA1077702 and SRA study SRP490212. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39607687) ↗
Study design
53 distinct titles, 13 of them repeated
HCT116_Cl6_shU1_Knockdown_D ×5 HCT116_Cl6_shU1_Recovery_D ×5 HCT116_Cl3_shU1_Recovery_D ×5 HCT116_Bulk_shD1_Baseline_D14 ×4 HCT116_Bulk_shD1_Knockdown_D14 ×4 HCT116_Cl6_shU1_Baseline_D ×2 HCT116_Cl3_shU1_Baseline_D ×2 HCT116_Cl3_shU1_Knockdown_D ×2 +5 more

Supports a case/control comparison: 16 samples read as cases, 24 as controls.

How we read this: Read from 79 sample titles: 53 distinct titles with little repetition. 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

+ 39 more — browse all 79 samples with per-sample file links →

Datasets on a similar topic

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.