Evidence map›Paper›PMID 27749837›Full record

ArticleNature methods2016

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Xingqi Chen, Ying Shen, Will Draper, Jason D Buenrostro, Ulrike Litzenburger, Seung Woo Cho, Ansuman T Satpathy, Ava C Carter, Rajarshi P Ghosh, Alexandra East-Seletsky and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
176citing papers in PubMed, 1 pooled it
10.4field-weighted citation impact, top 1% of its field
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

176 citing papers in PubMed, 1 synthesis or guideline pooled it, 281 citations in OpenAlex.

  1. Pooled it
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  3. Review
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  7. Article
  8. Advances in spatial omics for the analysis of prostate cancer.Analytical and bioanalytical chemistry · 2026
    Review
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116 more citing papers are in PubMed but not listed here.

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

14 authors at 4 institutions in 1 country.

Xingqi ChenCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Ying ShenCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Will DraperDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Jason D BuenrostroCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Ulrike LitzenburgerCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Seung Woo ChoCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Ansuman T SatpathyCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Ava C CarterCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Rajarshi P GhoshDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Alexandra East-SeletskyDepartment of Molecular and Cell Biology, University of California, Berkeley, California, USA.
Jennifer A DoudnaDepartment of Molecular and Cell Biology, University of California, Berkeley, California, USA.
William J GreenleafCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Jan T LiphardtDepartment of Bioengineering, Stanford University, Stanford, California, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Dynamic Systems (United States) · USStanford University · USHoward Hughes Medical Institute · USUniversity of California, Berkeley · US

Funding

Translational Oncology Research Program (Project-005)P30CA124435 · NCI · STANFORD UNIVERSITY · PI Melinda L. Telli · 2007 to 2026
$71.4M
INSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2M
Special EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2M
TRANS-NETWORK PROJECTSU54CA143836 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI LIPHARDT, JAN T. · 2009 to 2014
$15.1M
Deep Super-localization Microscopy and Effectively Unbleachable Labeling for 4D NucleomicsU01EB021237 · NIBIB · STANFORD UNIVERSITY · PI LIPHARDT, JAN T. · 2015 to 2017
$1.1M
NCI NIH HHS P30 CA124435NCI NIH HHS U54 CA143836NHGRI NIH HHS P50 HG007735NHGRI NIH HHS T32 HG000044NIBIB NIH HHS U01 EB021237
6 · The paper itself

Abstract

Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.

Indexed as

Genome, HumanHigh-Throughput Nucleotide SequencingCD4-Positive T-LymphocytesCell LineChromatinChromatin Assembly and DisassemblyDNA Transposable ElementsEpigenesis, GeneticFlow CytometryFluorescent DyesHeterocyclic Compounds, 4 or More RingsHumansImage Processing, Computer-AssistedMicroscopy, ConfocalNeutrophilsStaining and LabelingAtto590ChromatinDNA Transposable ElementsFluorescent DyesHeterocyclic Compounds, 4 or More RingsTn5 transposaseTransposases

Identifiers

PMID27749837
PMCPMC5509561
OpenAlexW2538772529

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.