Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq.

Rekha M Dhillon-Richardson, Alexandra K Haugan, Megan L Martik

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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.

Reactivation of an embryonic cardiac neural crest transcriptional profile during zebrafish heart regeneration.Proceedings of the National Academy of Sciences of the United States of America · 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

3 authors.

Rekha M Dhillon-RichardsonDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.

Alexandra K HauganDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.

Megan L MartikDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. martik@berkeley.edu.

Funding

Investigating the contributions of neural crest to adult regenerationR00HD100587 · NICHD · UNIVERSITY OF CALIFORNIA BERKELEY · PI MARTIK, MEGAN LEE · 2021 to 2023

$747k

NICHD NIH HHS R00 HD100587

6 · The paper itself

Abstract

Interactions between transcription factors and regulatory DNA can be described by gene regulatory networks. These networks provide a systems-level view of embryonic tissue development. Here, we describe a protocol for the isolation, identification, and experimental manipulation of tissue-specific cis-regulatory elements during zebrafish embryonic development using low-input ATAC-seq. With the methods described, genome-wide assessments of regulatory DNA in small populations of developing tissues can be identified, allowing for the construction of gene regulatory networks.

Indexed as

Chromatin Immunoprecipitation SequencingZebrafishAnimalsEmbryonic DevelopmentFemaleGene Regulatory NetworksAssay for transposase-accessible chromatin using sequencing (ATAC-seq)Embryonic DevelopmentEnhancer screeningFluorescence-activated cell sorting (FACS)Gene Regulatory NetworksZebrafish

Identifiers

PMID36427156

DOI10.1007/978-1-0716-2847-8_19

PMCPMC10198728

What OpenQuestion holds

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Registered trials

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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.