Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data.

Meghan V Petrie, Yiwei He, Yan Gan, Andrew Zachary Ostrow, Oscar M Aparicio

Abstract read

In one paragraph

Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

FTO depletion does not alter mbioRxiv : the preprint server for biology · 2025
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Meghan V PetrieMolecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA.

Yiwei HeMolecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA.ORCID 0000-0002-0004-7242

Yan GanMolecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA.

Andrew Zachary OstrowMolecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA.

Oscar M AparicioMolecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA.ORCID 0000-0002-5591-0277

Funding

Regulation of Chromosomal DNA Replication Dynamics in S. CerevisiaeR01GM065494 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI APARICIO, OSCAR M · 2003 to 2022

$6.9M

NIGMS NIH HHS R01 GM065494

6 · The paper itself

Abstract

Chromatin ImmunoPrecipitation (ChIP) is a widely used method for the analysis of protein-DNA interactions in vivo; however, ChIP has pitfalls, particularly false-positive signal enrichment that permeates the data. We have developed a new approach to control for non-specific enrichment in ChIP that involves the expression of a non-genome-binding protein targeted in the IP alongside the experimental target protein due to the sharing of epitope tags. ChIP of the protein provides a "sensor" for non-specific enrichment that can be used for the normalization of the experimental data, thereby correcting for non-specific signals and improving data quality as validated against known binding sites for several proteins that we tested, including Fkh1, Orc1, Mcm4, and Sir2. We also tested a DNA-binding mutant approach and showed that, when feasible, ChIP of a site-specific DNA-binding mutant of the target protein is likely an ideal control. These methods vastly improve our ChIP-seq results in

Indexed as

Saccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsBinding SitesCell Cycle ProteinsChromatin ImmunoprecipitationChromatin Immunoprecipitation SequencingDNAForkhead Transcription FactorsProteinsSequence Analysis, DNACell Cycle ProteinsDNAFkh1 protein, S cerevisiaeForkhead Transcription FactorsProteinsSaccharomyces cerevisiae Proteinschromatin immunoprecipitationcontrolsDNA-binding proteingenomereplication origins

Identifiers

PMID37298223

DOI10.3390/ijms24119271

PMCPMC10252487

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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.