NABEC: North American Brain Expression Consortium
Ontology highlight
ABSTRACT: This study utilized neurologically normal control samples deposited in North American Brain Expression Consortium (NABEC). This top-level study, phs001300, makes available all phenotype data of the NABEC study participants.
In addition, molecular data of six sub-studies are available through dbGaP:
SECONDARY ACCESSION(S): PRJNA375877PRJNA375878
REPOSITORIES: dbGaP
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| GapExchange_phs001300.v1.p1.xml | Xml | |||
| dbGaPEx2.1.5.xsd | Other | |||
| Study_Report.phs001300.NABEC.v1.p1.MULTI.pdf | ||||
| manifest_phs001300.NABEC.v1.p1.c1.GRU.pdf | ||||
| datadict_v2.xsl | Other |
Items per page: 5 1 - 5 of 126 |
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Project description:This SuperSeries is composed of the SubSeries listed below. The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1
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<p>This data includes that from subjects both banked in the <a href="http://ccr.coriell.org/Sections/Collections/NINDS/?SsId=10">
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<!-- <p><b>Important links to apply for individual-level data</b>
<ol>
<li><a href="http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000102.v1.p1" target="_blank">Data Use Certification Requirements (DUC)</a></li>
<li><a href="http://view.ncbi.nlm.nih.gov/dbgap-controlled" target="_blank">Apply here for controlled access to individual level data</a></li>
<li><a href="GetPdf.cgi?id=phd000582" target="_blank">Participant Protection Policy FAQ</a></li>
</ol>
</p> -->
<p>This study utilized the <a href="./study.cgi?id=phs000005">NINDS Repository Cerebrovascular/Stroke Study</a>,
and <a href="./study.cgi?id=phs000004">neurologically normal controls</a> from the sample population which are banked in the National
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Project description:A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on mRNA expression distinct human brain regions. We show that brain tissues may be readily distinguished based on expression profile. We find an abundance of genetic cis regulation mRNA expression. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249 Because of our interest in genomic regulation of expression and neurological disorders we embarked upon a series of experiments to provide a brain region-specific contextual framework for genetic and epigenetic regulation of gene expression. We obtained frozen brain tissue from the cerebellum and frontal cortex from 396 subjects (total 911 tissue samples).
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Project description:In order to gain a global molecular perspective on how the human genome gives rise to the brain, we explore the temporal dynamics and genetic control of transcription in human dorsolateral prefrontal cortex in an extensive series of brain tissue from fetal development through aging. We discover a wave of gene expression changes occurring during fetal development which are reversed in early postnatal life. One half century later in life, this phenomenon is mirrored in aging as well as neurodegeneration. While we identify thousands of robust associations of individual genetic polymorphisms with gene expression, we also demonstrate that there is no association between the total extent of genetic differences between subjects and the global similarity of their transcriptional profiles. Hence, the human genome produces a consistent molecular architecture in the prefrontal cortex, despite millions of genetic differences across individuals and races. To enable further discovery, this entire dataset is freely available (GEO). RNA from 269 human prefrontal cortex samples ranging from fetal development (negative ages) through aging (80 years) were analyzed on custom 2-color microarrays from the National Human Genome Research Institute (NHGRI) microarray core facility using a reference RNA comprised of a pool of all samples. SNP genotype data for these subjects can be found in dbGAP under Study ID *phs000417.v1.p1* http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000417.v1.p1 Both the gene expression and SNP data from this study can be interrogated gene-by-gene with a biologist-friendly stand-alone application available at http://www.libd.org/braincloud . The original publication of this data appeared in the Oct. 27th 2011 volume of Nature: http://www.nature.com/nature/journal/v478/n7370/full/nature10524.html .
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<p>This study utilized the well characterized <a href="./study.cgi?id=phs000003">collection of North American Caucasians
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population which are banked in the National Institute of Neurological Disorders and Stroke (NINDS Repository) collection
for a first stage whole genome analysis. Genome-wide, single nucleotide polymorphism (SNP) genotyping of these publicly
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<p>The NINDS repository was established in 10-2001 towards the goal of developing standardized, broadly useful diagnostic
and other clinical data and a collection of DNA and cell line samples to further advances in gene discovery of neurological
disorders. All samples, phenotypic, and genotypic data are available to the research community including to academics and
industry scientists. In addition, well characterized neurologically normal control subjects are a part of the collection.
This collection formed the basis of this first stage study by Fung et al., and the expanded study by Simon-Sanchez et al.
The genotyping data was generated and provided by the laboratory of Dr. Andrew Singleton NIA, and Dr. John Hardy
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<p><b>Important links to apply for individual-level data</b>
<ol>
<li><a href="http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000089.v3.p2" target="_blank">Data Use Certification Requirements (DUC)</a></li>
<li><a href="http://view.ncbi.nlm.nih.gov/dbgap-controlled" target="_blank">Apply here for controlled access to individual level data</a></li>
<li><a href="GetPdf.cgi?id=phd000577" target="_blank">Participant Protection Policy FAQ</a></li>
</ol>
</p>
| phs000089.v3.p2 | EGA