Gene Expression Nebulas
A data portal of transcriptomic profiles across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA231202: RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms, and GTPase binding in bipolar disorder

Source: NCBI / GSE53239
Submission Date: Dec 11 2013
Release Date: Jan 08 2014
Update Date: May 15 2019

Summary: See "Akula et al., Molecular Psychiatry in Press". RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality post-mortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false-discovery rate of <5%, we detected 5 differentially-expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, PROM1/CD133 and ABCG2 play important roles in neuroplasticity. We also show for the first time differential expression of long non-coding RNAs (lncRNAs) in BD. DE transcripts include those of SRSF5 and RFX4, which along with lncRNAs play a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology (GO) categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.

Overall Design: Brain transcriptome in bipolar disorder

GEN Datasets:
GEND000014
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Total RNA was extracted from the dorsolateral prefrontal cortex (Brodmann area 46) of post-mortem brain tissue of 11 BD cases and 11 healthy controls
Library Construction Protocol: Illumina HiSeq 2000 with paired-end flow cell.
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina Genome Analyzer II; Illumina HiSeq 1000
Strand-Specific: Unspecific
Publications
RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.
Molecular psychiatry . 2014-01-07 [PMID: 24393808]
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