Evidence map›Paper›PMID 38014002›Full record

ArticleResearch square2023

Integrated multi-omics single cell atlas of the human retina.

Jin Li, Jun Wang, Ignacio L Ibarra, Xuesen Cheng, Malte D Luecken, Jiaxiong Lu, Aboozar Monavarfeshani, Wenjun Yan, Yiqiao Zheng, Zhen Zuo and 12 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Jin LiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.
Jun WangDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.
Ignacio L IbarraInstitute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
Xuesen ChengDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.ORCID 0000-0002-0678-4411
Malte D LueckenInstitute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.ORCID 0000-0001-7464-7921
Jiaxiong LuDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.
Aboozar MonavarfeshaniCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.
Wenjun YanCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.ORCID 0000-0003-3568-4265
Yiqiao ZhengDepartment of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States.ORCID 0000-0003-4133-0439
Zhen ZuoDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.
Samantha Lynn Zayas ColbornLions Eye Bank of Texas, Baylor College of Medicine, Houston, Texas, United States.
Berenice Sarahi CortezLions Eye Bank of Texas, Baylor College of Medicine, Houston, Texas, United States.
Leah A OwenJohn A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States.
Nicholas M TranDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.
Karthik ShekharDepartment of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California, United States.
Joshua R SanesCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.ORCID 0000-0001-8926-8836
J Timothy StoutDepartment of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, United States.
Shiming ChenDepartment of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States.
Yumei LiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.ORCID 0000-0002-4908-8459
Margaret M DeAngelisDepartment of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States.
Fabian J TheisInstitute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.ORCID 0000-0002-2419-1943
Rui ChenDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.ORCID 0000-0002-4387-9735

Funding

WASHINGTON UNIVERSITY CENTER VISION RESEARCHP30EY002687 · NEI · WASHINGTON UNIVERSITY · PI Steven Bassnett · 1985 to 2026
$18.4M
Vulnerable and Resilient Cells in Retinal DegenerationR01EY012543 · NEI · WASHINGTON UNIVERSITY · PI SHIMING CHEN, Philip Raymond Williams · 2000 to 2026
$12.2M
Comprehensive Classification Of Neuronal Subtypes By Single Cell TranscriptomicsU01MH105960 · NIMH · HARVARD UNIVERSITY · PI REGEV, AVIV, SANES, JOSHUA R · 2014 to 2016
$4.5M
Understanding and treating CRX-linked retinopathiesR01EY032136 · NEI · WASHINGTON UNIVERSITY · PI CHEN, SHIMING · 2021 to 2025
$1.9M
CIS-REGULATORY MECHANISMS UNDERLYING RETINOPATHYR01EY027784 · NEI · WASHINGTON UNIVERSITY · PI CHEN, SHIMING, COHEN, BARAK A · 2017 to 2020
$1.4M
High Throughput Genomic Sequencer at BCM Core FacilityS10OD023469 · OD · BAYLOR COLLEGE OF MEDICINE · PI CHEN, RUI · 2017 to 2017
$600k
Defining cell types of foveal and peripheral retina by high-throughput, single-celltranscriptional profilingR21EY028633 · NEI · HARVARD UNIVERSITY · PI DO, MICHAEL TRI HOANG, SANES, JOSHUA R · 2018 to 2019
$487k
NEI NIH HHS P30 EY002687NEI NIH HHS R01 EY012543NEI NIH HHS R01 EY027784NEI NIH HHS R01 EY032136NEI NIH HHS R21 EY028633NIH HHS S10 OD023469NIMH NIH HHS U01 MH105960
6 · The paper itself

Abstract

Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.

Identifiers

PMID38014002
PMCPMC10680922

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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.