Single Cell Analysis Program - Transcriptome (SCAP-T: UCSD): Single-Cell Sequencing and In Situ Mapping of RNA Transcripts in Human Brains

A comprehensive characterization of transcriptional diversity and heterogeneity of the human cortex is crucial to understand its functions in healthy and disease conditions. The diversity and cellular states of the densely packed cellular network in the cortex can be accurately captured by the transcriptional activities of individual cells. An overarching goal is to establish a high-resolution three dimensional map of all transcriptional activities in the human cortex. In this project we will generate 10,000 sets of full transcriptome data on single cells and nuclei from three areas (visual, temporal, prefrontal) of the human cortex. In addition, we will develop a novel RNA in situ sequencing method, and apply it to cortex sections to map and quantify at least 500 transcripts directly within the tissue at a spatial resolution of single cells. Using the spatial information of these ~500 transcripts as fingerprints, we will computationally map the additional transcripts in the 10,000 full transcriptome data sets to the cortex sections at the single-cell resolution, which will yield a highly comprehensive map of transcriptional activities of the human cortex in an unprecedented level of resolution. PUBLIC HEALTH RELEVANCE: We will establish a three dimensional map of all transcriptional activities at the single-cell resolution in three areas of human cortex. Such a comprehensive characterization of transcriptional diversity and heterogeneity of the human cortex is crucial to understand its functions. It will enable the identification of accurate biomarkers for prognosis and diagnosis brain disorders.

This first data release of SCAP-T (UCSD) includes the detailed phenotype information, experimental protocols, QC information, RNA-sequencing data and NGS results for 497 single neuronal nuclei from human brain. The SCAP-T data portal provides a customized interface for users to quickly identify and retrieve files by phenotypes, and data properties such as sequencing facility or coverage. For more information about the SCAP-T study and the data portal, please visit http://www.scap-t.org.

• Study Weblinks:
  • SCAP-T
• Study Design:
  • Methods
• Study Type:
  • Single Cell Analysis
• Total number of consented subjects: 1
• Subject Sample Telemetry Report (SSTR)

• Primary Phenotype: Prefrontal Cortex
• Visual Cortex
• Cerebral Cortex

• Principal Investigator
  • Kun Zhang. University of California, San Diego, CA, USA.
• Funding Sources
  • 1U01MH098977-01. National Institutes of Health, Bethesda, MD, USA.