ArticleGenome research2021
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 23 citations in OpenAlex.
- Article
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells.G3 (Bethesda, Md.) · 2026Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation.bioRxiv : the preprint server for biology · 2025Article
- Identification of human RNA Polymerase II interactors at early stages of transcription.bioRxiv : the preprint server for biology · 2025Article
- Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.Bioinformatics (Oxford, England) · 2025Article
- Article
- Benchmark of chromatin-protein interaction methods in haploid round spermatids.Frontiers in cell and developmental biology · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.bioRxiv : the preprint server for biology · 2024Article
- Systematic identification of post-transcriptional regulatory modules.Nature communications · 2024Article
- Antibody characterization is critical to enhance reproducibility in biomedical research.eLife · 2024Review
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA.American journal of human genetics · 2024Article
- The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping.Briefings in bioinformatics · 2024Article
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.Nucleic acids research · 2024Article
- AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization.Cells · 2022Article
- PEGR: a flexible management platform for reproducible epigenomic and genomic research.Genome biology · 2022Article
- STENCIL: A web templating engine for visualizing and sharing life science datasets.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
25 authors at 5 institutions in 1 country.
Funding
Abstract
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. Eight hundred eighty-seven unique antibodies against 681 unique human transcription factors (TFs) were assayed by ultra-high-resolution ChIP-exo/seq, generating approximately 1200 ChIP-exo data sets, primarily in a single pass in one cell type (K562). Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed high-confidence target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that were distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We show and discuss the metrics and challenges to antibody validation in chromatin-based assays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.