Evidence map›Paper›PMID 37546900›Full record

ArticlebioRxiv : the preprint server for biology2023

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells.

Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 12 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 1 country.

Tianming ZhouComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Ruochi ZhangComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Deyong JiaDepartment of Urology, University of Washington, Seattle, WA 98195, USA.
Raymond T DotyDivision of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
Adam D MundayDivision of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
Daniel GaoInstitute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
Li XinDepartment of Urology, University of Washington, Seattle, WA 98195, USA.
Janis L AbkowitzDivision of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
Zhijun DuanDivision of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
Jian MaComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
University of Washington · USCarnegie Mellon University · USBroad Institute · USPomona College · US

Funding

Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4M
UW 4-Dimensional Genomic Organization of Mammalian Embryogenesis CenterUM1HG011586 · NHGRI · UNIVERSITY OF WASHINGTON · PI DISTECHE, CHRISTINE M., NOBLE, WILLIAM STAFFORD · 2020 to 2024
$10.3M
Impact of Methamphetamine Use on the HIV Nucleome in Individuals on Antiretroviral TherapyR61DA047010 · NIDA · UNIVERSITY OF WASHINGTON · PI DUAN, ZHIJUN, MULLINS, JAMES IVAN · 2018 to 2020
$3.1M
Computational Methods for Next-Generation Comparative GenomicsR01HG007352 · NHGRI · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI MA, JIAN · 2014 to 2023
$2.8M
Computational methods for studying single-cell 3D genomeR01HG012303 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI DUAN, ZHIJUN, MA, JIAN · 2022 to 2025
$2.2M
Spatial omics technologies to map the senescent cell microenvironmentUG3CA268202 · NCI · BROWN UNIVERSITY · PI MA, JIAN, NERETTI, NICOLA · 2021 to 2022
$916k
Single-cell multiomic methods for studying genome structure and functionR56HG013092 · NHGRI · UNIVERSITY OF WASHINGTON · PI DUAN, ZHIJUN, MA, JIAN · 2023 to 2023
$400k
NCI NIH HHS UG3 CA268202NHGRI NIH HHS R01 HG007352NHGRI NIH HHS R01 HG012303NHGRI NIH HHS R56 HG013092NHGRI NIH HHS UM1 HG011586NHGRI NIH HHS UM1 HG011593NIDA NIH HHS R61 DA047010
6 · The paper itself

Abstract

The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed

Identifiers

PMID37546900
PMCPMC10401946
OpenAlexW4385256317

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.