Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA593861

PRJNA593861: Single cell transcriptome profiling of the human alcohol-dependent brain samples.

Source: NCBI / GSE141552
Submission Date: Dec 05 2019
Release Date: Apr 14 2020
Update Date: Apr 14 2020

Summary: Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex samples of alcoholic and control individuals. Libraries were prepared with 10X Genomics platform and sequenced using NovaSeq 6000.

Overall Design: Single nucleus RNA sequencing (snRNA-seq) from prefrontal cortex of 3 alcoholic and 4 control individuals.

GEN Datasets:
GEND000129
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
Growth Protocol: -
Treatment Protocol: Alcoholic and control donors were selected to be as close as possible in terms of age, sex, post-mortem interval (PMI), pH of tissue, and cause of death
Extract Protocol: Nuclei were isolated from tissue based on a modified version of Luciano Martelotto's Customer-Developed Protocol provided on the 10XGenomics website.
Library Construction Protocol: Libraries were prepared using the 10X Genomics 3' Single Cell Gene Expression protocol. Paired-end sequencing of the libraries was conducted using a NovaSeq 6000 with an S2 chip (100 cycles).
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Single cell transcriptome profiling of the human alcohol-dependent brain.
Human molecular genetics . 2020-05-01 [PMID: 32142123]