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Study Description

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.

The SCAP-T (UCSD) data sets include the detailed phenotype information, experimental protocols, QC information, RNA-sequencing data and NGS results from human heart and human brain cells. The first data release includes 497 single neuronal nuclei from human brain. The second data release includes an additional 561 single neuronal nuclei from human brain. The third data release includes an additional 761 single neuronal nuclei from human brain. The fourth data release did not include any changes to the UCSD dataset but rather marked a correction to the USC dataset. The fifth data release includes an additional 2055 single neuronal nuclei from human brain. The sixth data release includes an additional 42 single neuronal nuclei from human brain, bringing the total number of single cells available to 3916. The seventh data release includes an additional 1245 single neuronal nuclei from human brain, bringing the total number of single cells available to 5161. 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 all these single cells. For more information about the SCAP-T study and the data portal, please visit http://www.scap-t.org.

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Publicly Available Data (Public ftp)

Note: Access to publicly available data is available on the public ftp site for study phs000833.v7.p1

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
RNA Sequencing Illumina HiSeq 2000 N/A N/A
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