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Impact of Chromatin Immunoprecipitation Crosslinking Conditions on Selective Genomic Interactions by NF‐κB Family Members

GSE249834 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 21 samples Submitted 2024/08/11 Platform GPL21493Platform GPL13112
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 21 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
21 samples: 21 samples, each with a distinct title — no replicated groupsGroups 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
Examining NF-κB genomic interactions by ChIP-seq and CUT&TagbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
The ability to capture protein: DNA interactions in a quantitative, high-resolution, and temporal manner in the cell context is crucial for elucidating the mechanisms underlying transcriptional regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used technique that enables the study of histone modifications and genome-wide interactions of transcription factors and chromatin regulators.
Read the full summary ↓
Although ChIP-seq generates a vast amount of information, crosslinking conditions need to be carefully evaluated to minimize the capture of non-specific interactions. In this study, we conduct an in-depth analysis to evaluate the impact of crosslinking conditions on ChIP-seq results for two NF-kB family members, RelA and c-Rel. We titrate two commonly used chemical crosslinkers, formaldehyde and DSG. We demonstrate that while raising the crosslinking concentrations increases the total number of binding sites and the strength of the binding signal, high crosslinking conditions lead to an abundance of interactions detected at locations that lack anticipated motifs or annotations to potential NF-kB target genes. Our findings emphasize the importance of a comprehensive evaluation of ChIP-seq results and a cautious evaluation of chemical crosslinking conditions. Moreover, we compare ChIP-seq to CUT&TAG, a newer technique that does not require crosslinking. This comparison revealed strongly overlapping genomic interactions between the two methods. However, both methods display evidence of a large number of non-specific signals that exhibit little overlap between the two methods.
Published in
Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag
Daly AE, Schiffman A, Hoffmann A et al. · bioRxiv : the preprint server for biology 2024 · PMID 39185161 · doi:10.1101/2024.08.11.607521
This dataset
Open GSE249834 in finder → Find more mouse 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 GSE249834_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 PRJNA1050825 and SRA study SRP477214. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39185161) ↗
Study design
21 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 21 sample titles: 21 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
Datasets on a similar topic

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