University of Washington Developmental Single Cell Atlas

We set out to generate a human cell atlas of both gene expression and chromatin accessibility using tissues obtained during development. In this study, we applied an assay for single cell profiling of gene expression based on three-level combinatorial indexing (sci-RNA-seq3) to 121 fetal tissue samples representing 15 organs, altogether profiling transcription in over 4 million single cells. In parallel, we devised an improved assay for single cell profiling of chromatin accessibility also based on three-level combinatorial indexing (sci-ATAC-seq3). We applied this method to 53 fetal tissue samples representing 15 organs, altogether profiling on the order of one million single cells. From these data, we identify and characterize diverse human cell types and annotate them with respect to marker genes, expression and regulatory modules. These data comprise a rich resource for the exploration of human biology.

• Study Weblinks:
  • Brotman Baty Single Cell Atlases
• Study Design:
  • Control Set
• Study Type:
  • Control Set
• dbGaP estimated ancestry using GRAF-pop
• Total number of consented subjects: 38
• Subject Sample Telemetry Report (SSTR)

• BioProject
• Sequence Read Archive
• MeSH

Postmortem interval <24 hours.

• Primary Phenotype: Human Development
• Gene Expression
• Gene Expression Regulation

• Principal Investigator
  • Ian Glass, MD. University of Washington, Seattle, WA, USA.
  • Jay Shendure. University of Washington, Seattle, WA, USA.
  • Cole Trapnell. University of Washington, Seattle, WA, USA.
• Funding Source
  • R24HD000836. National Institute of Child Health and Human Development.
  • Jay Shendure. Brotman Baty Institute for Precision Medicine.
  • Cole Trapnell. Brotman Baty Institute for Precision Medicine.