Evidence map›Paper›PMID 40364978›Full record

ArticleBio-protocol2025

ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for

Kris G Alavattam, Bradley M Dickson, Rina Hirano, Rachel Dell, Toshio Tsukiyama

Abstract read
In one paragraph

Article in Bio-protocol, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Kris G AlavattamBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Bradley M DicksonDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
Rina HiranoBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Rachel DellBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Toshio TsukiyamaBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Funding

Molecular mechanisms and functions of global chromatin controlR35GM139429 · NIGMS · FRED HUTCHINSON CANCER RESEARCH CENTER · PI TOSHIO TSUKIYAMA · 2021 to 2026
$4.6M
NIGMS NIH HHS R35 GM139429
6 · The paper itself

Abstract

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a widely used technique for genome-wide analyses of protein-DNA interactions. This protocol provides a guide to ChIP-seq data processing in

Indexed as

BioinformaticsChIP-seqData processingNormalizationReproducibilityS. cerevisiaeSignal scalingsiQ-ChIPSpike-in

Identifiers

PMID40364978
PMCPMC12067309

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

None linked

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.