Single Cell Multiome Atlas of the Human Developing Retina

Rui Chen, Zhen Zuo, Xuesen Cheng, Salma Ferdous, Jianming Shao, Jin Li, Jiaxiong Liu, Antonio Jacobo, Yumei Li, Ala Moshiri

Abstract

Development of retina is under tight temporal and spatial control. To gain insights of the molecular underpinning of this process, we generated a single-nuclei multiome atlas of the human developing retina with approximately 300,000 nuclei from 12 donors aged between 10 and 23 weeks post-conception with matched macula and peripheral regions from each donor. This atlas captures all major cell classes and over 50 cell types in the retina along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitor cells to a hierarchical development during the later stages of cell type specification. Both known and novel candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between macular and peripheral retina indicate a largely consistent yet distinct developmental pattern. In particular, the retinoic acid pathway emerges as a potential key driver for retinal patterning. This multiome developing retina atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscape during development, presenting an invaluable resource for deeper insights into retinal development and associated diseases.

Datasets

1. snRNA-seq of the developing human retina
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
donor_id
self_reported_ethnicity_ontology_term_id
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_derivation_process
suspension_dissociation_reagent
suspension_uuid
suspension_type
tissue_handling_interval
library_uuid
assay_ontology_term_id
sequencing_platform
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
sex_ontology_term_id
subclass
majorclass
study_name
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh38226506 cells
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Single Cell Multiome Atlas of the Human Developing Retina

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Dataset 1
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Source data

https://cellxgene.cziscience.com/collections/5900dda8-2dc3-4770-b604-084eac1c2c82

Alias names

Cite this study

Chen, R., Zuo, Z., Cheng, X., Ferdous, S., Shao, J., Li, J., Liu, J., Jacobo, A., Li, Y. and Moshiri, A., 2023. Single Cell Multiome Atlas of the Human Developing Retina. https://doi.org/10.21203/rs.3.rs-3417373/v1