An integrated transcriptomic cell atlas of human neural organoids

Version

February 11th, 2025

DOI

https://doi.org/10.57772%2Fcap.lr1qubc8lvq53byicflpmnedecs2.580

The Human Cell Atlas data provides the “recipe” for tissue engineering, including organoids. Human organoids – three-dimensional structures of cells that recapitulate organ development in vitro – hold tremendous potential for biomedical applications. They provide tractable models of human physiology and pathology, thereby enabling interventional studies that are difficult or impossible to conduct in human subjects, and reducing the need for animal experiments. Moreover, they can provide patient-specific “avatars” for drug development and personalized therapies, and they help advance regenerative medicine, with the ultimate goal of aiming towards regenerative medicine, and producing functional biological structures that can be transplanted into patients.

Single-cell epigenome/transcriptome sequencing and spatial profiling can provide a comprehensive assessment of cell composition and cell states within organoids, enabling a comparison to matched primary tissue samples. These comparisons can catalyse the development of better organoid protocols. The Organoid Cell Atlas will foster the production, quality control, dissemination, and utilization of single-cell data for human organoids, and it will connect such datasets with the comprehensive profiles of primary tissue that are being generated within the HCA.

Scientific Journal DOI: https://doi.org/10.1038/s41586-024-08172-8
External URLs: https://doi.org/10.5281/zenodo.11203684; https://devsystemslab.github.io/HNOCA-tools/; https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847

Datasets

The Human Neural Organoid Atlas

The HNOCA includes data from 36 neural organoid datasets and includes harmonised cell type annotations, as well as curated biological, and technical metadata. The datasets in the HNCOA were integrated using scPoli. The HNOCA can be used as a reference to map new datasets onto using scArches, allowing the transfer of the harmonized cell-type labels to any new dataset.

Explore Dataset

assay: 10x 3' v3
10x 3' v2
Drop-seq
10x multiome
BD Rhapsody Whole Transcriptome Analysis
SPLiT-seq
Quartz-seq
Smart-seq2
tissue: telencephalon
cerebral cortex
brain
midbrain tegmentum
midbrain tectum
arcuate nucleus of hypothalamus
ventral part of telencephalon
hindbrain
choroid plexus
cerebellum
dorsal plus ventral thalamus
organism: Homo sapiens
disease: normal

855,360

528,356

90,701

79,506

77,315

49,270

Astrocyte

48,956

15,433

NC Derivatives

9,718

OPC

8,325

2,451

PSC

2,187

+2 sets of cell labels