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Genome-wide mapping of native G-loops in living cells

GSE254764 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 28 samples Submitted 2024/07/25 Platform GPL24676Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 28 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
Mus musculus (mouse)
Samples
28 samples: 12 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
Genome-wide mapping of native co-localized G4s and R-loops in living cellseLife · 2024
Summary (written by the submitters)
G-quadruplex (G4) are four‑stranded DNA secondary structures that form in guanine‑rich regions of the genome, which can enhance or repress gene expression. An R-loop is a special triple-stranded nucleic acid structure formed when nascent RNA invades double-stranded DNA (dsDNA) during transcription. G-loops are constituted by one or more DNA G4 on one strand and a stable RNA/DNA hybrid on the other.
Read the full summary ↓
We developed the HepG4-seq for mapping the native G4s and the HBD-seq for mapping native R-loops. We combined the HepG4-seq and HBD-seq to profile the genomic native G-loops, which are regions co-occupied by both native G4s and R-loops, in both HEK293 cells and mouse embryonic stem cells (mESCs).
Published in
Genome-wide mapping of native co-localized G4s and R-loops in living cells
Liu T, Shen X, Ren Y et al. · eLife 2024 · PMID 39392462 · doi:10.7554/eLife.99026
This dataset
Open GSE254764 in finder → Find more 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 GSE254764_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 PRJNA1071642 and SRA study SRP487229. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39392462) ↗
Study design
12 conditions, mostly in duplicate
HEK293_BG4-seq_without_Hemin ×2 HEK293_BG4-seq_with_Hemin ×2 HEK293_HepG4-seq ×2 HEK293_HepG4-seq_Non-label_Ctrl ×2 HEK293_HBD-seq ×2 mESC_HepG4-seq ×2 mESC_HepG4-seq_Non-label_Ctrl ×2 mESC_HBD-seq ×2 +8 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 28 sample titles; they account for 24 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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