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, Samantha Lynn Zayas Colborn, Berenice Sarahi Cortez, Leah A. Owen, Nicholas M. Tran, Karthik Shekhar, Joshua R. Sanes, J. Timothy Stout, Shiming Chen, Yumei Li, Margaret M. DeAngelis, Fabian J. Theis, Rui Chen

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 We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types.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.

Datasets

1. scRNA-seq of human retina - all cells
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
donor_id
donor_age
self_reported_ethnicity_ontology_term_id
donor_cause_of_death
donor_living_at_sample_collection
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
sample_derivation_process
sample_source
tissue_type
suspension_depletion_factors
suspension_depleted_cell_types
suspension_derivation_process
suspension_dissociation_reagent
suspension_dissociation_time
suspension_enriched_cell_types
suspension_enrichment_factors
suspension_percent_cell_viability
suspension_uuid
suspension_type
tissue_handling_interval
library_uuid
assay_ontology_term_id
library_starting_quantity
sequencing_platform
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
majorclass
group2
group3
study_name
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh38265767 cells
Preview
Integrated multi-omics single cell atlas of the human retina

Analyze this study

Dataset 1
Download OmnibusX

Source data

https://cellxgene.cziscience.com/collections/4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e

Alias names

Single cell atlas of the human retina, PMID38014002, PMC10680922

Cite this study

Li, J., Wang, J., Ibarra, I.L., Cheng, X., Luecken, M.D., Lu, J., Monavarfeshani, A., Yan, W., Zheng, Y., Zuo, Z. and Colborn, S.L.Z., 2023. Integrated multi-omics single cell atlas of the human retina. Research Square. https://doi.org/10.1101/2023.11.07.566105