Evidence map›Paper›PMID 30936163›Full record

ArticleGenome research2019

The accessible chromatin landscape of the murine hippocampus at single-cell resolution.

John R Sinnamon, Kristof A Torkenczy, Michael W Linhoff, Sarah A Vitak, Ryan M Mulqueen, Hannah A Pliner, Cole Trapnell, Frank J Steemers, Gail Mandel, Andrew C Adey

Abstract read
In one paragraph

Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.

0numbers the graph read from it
0cells of the map it votes in
44citing 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

44 citing papers in PubMed.

  1. Article
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  6. Review
  7. Article
  8. Article
  9. Article
  10. The Hypothalamic Epigenetic Landscape in Dietary Obesity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024
    Article
  11. Article
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  14. Article
  15. Article
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  18. Article
  19. Review
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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

10 authors.

John R Sinnamon *The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.ORCID 0000-0001-6818-9389
Kristof A Torkenczy *Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.
Michael W LinhoffThe Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.
Sarah A VitakDepartment of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.
Ryan M MulqueenDepartment of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.
Hannah A PlinerDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0003-1484-6501
Cole TrapnellDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-8105-4347
Frank J SteemersIllumina, Incorporated, San Diego, California 92122, USA.
Gail MandelThe Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.ORCID 0000-0003-2085-4516
Andrew C AdeyDepartment of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.ORCID 0000-0001-7648-8717

Funding

University of Washington Center for Nuclear Organization and FunctionU54DK107979 · NIDDK · UNIVERSITY OF WASHINGTON · PI NOBLE, WILLIAM STAFFORD, SHENDURE, JAY ASHOK · 2015 to 2019
$11.8M
Pulmonary Macrophage Transplantation for Pulmonary Alveolar ProteinosisR01HL118342 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI TRAPNELL, BRUCE C, TRAPNELL, BRUCE COLSTON · 2014 to 2021
$4.5M
New roles for REST during brain maturationR01NS099374 · NINDS · OREGON HEALTH & SCIENCE UNIVERSITY · PI MANDEL, GAIL · 2017 to 2021
$2.6M
Charting the regulatory topography of the cell differentiation landscape with single-cell RNA-Seq.DP2HD088158 · NICHD · UNIVERSITY OF WASHINGTON · PI TRAPNELL, BRUCE COLSTON · 2015 to 2015
$2.3M
Defining the epigentic landscape at single cell resolutionR35GM124704 · NIGMS · OREGON HEALTH & SCIENCE UNIVERSITY · PI ADEY, ANDREW · 2017 to 2021
$2.3M
Epigenetic tools and resources for cell-type and spatial analysis of individual mammalian non-neuronal cellsR01DA047237 · NIDA · OREGON HEALTH & SCIENCE UNIVERSITY · PI ADEY, ANDREW · 2018 to 2020
$1.7M
NHLBI NIH HHS R01 HL118342NICHD NIH HHS DP2 HD088158NIDA NIH HHS R01 DA047237NIDDK NIH HHS U54 DK107979NIGMS NIH HHS R35 GM124704NINDS NIH HHS R01 NS099374
6 · The paper itself

Abstract

Here we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq); a software suite,

Indexed as

AnimalsCell LineageCell NucleusCells, CulturedChromatinEpigenomicsHippocampusMiceNeuronal PlasticityPyramidal CellsSequence Analysis, DNASingle-Cell AnalysisTransposasesChromatinTransposases

Identifiers

PMID30936163
PMCPMC6499306

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.