GEO series
Impact of Chromatin Immunoprecipitation Crosslinking Conditions on Selective Genomic Interactions by NF‐κB Family Members
GSE249834
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
21 samples
Submitted 2024/08/11
Platform GPL13112Platform GPL21493
Summary
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. 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
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
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Direct links to NCBI, no account and no request form: the whole study as GSE249834_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 21 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1050825 and SRA study SRP477214. Searching any of these in the dataset finder brings you back here.
Study design
21 conditions, each sampled once — no replicated groups
Read from 21 sample titles: 21 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM7965588 cRel_0mM_DSG
- GSM7965589 cRel_1mM_DSG
- GSM7965590 cRel_2mM_DSG
- GSM7965591 cRel_4mM_DSG
- GSM7965592 RelA_0mM_DSG
- GSM7965593 RelA_1mM_DSG
- GSM7965594 RelA_2mM_DSG
- GSM7965595 RelA_4mM_DSG
- GSM7965596 DSG_Input
- GSM7965597 cRel_0.0_PFA
- GSM7965598 cRel_0.5_PFA
- GSM7965599 cRel_1.0_PFA
- GSM7965600 cRel_2.0_PFA
- GSM7965601 RelA_0.0_PFA
- GSM7965602 RelA_0.5_PFA
- GSM7965603 RelA_1.0_PFA
- GSM7965604 RelA_2.0_PFA
- GSM7965605 PFA_Input
- GSM7965606 CUT&TAG_RelA_15min
- GSM7965607 CUT&TAG_RelA_45min
- GSM7965608 CUT&TAG_RelA_60min
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