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ID
45442
Description
Principal Investigator: Nenad Sestan, MD, PhD, Yale University, New Haven, CT, USA MeSH: Brain Diseases,Growth and Development,Aging https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000755 The NIH-funded BrainSpan (www.brainspan.org) and PsychENCODE (www.psychencode.org). Consortia sought to generate and analyze multi-dimensional genomics data from the developing and adult human brain in healthy and disease states. One of the main goals has been to perform large-scale and integrated analysis of the genome, transcriptome, and epigenome of the human brain to broaden our understanding of human neurodevelopment. This dataset consists of sixteen regions, including eleven neocortical areas, of human donors of both sexes and various ethnic groups. In the first stage of this project, we provide the genome-wide exon-level transcriptome data generated using the Affymetrix GeneChip Human Exon 1.0 ST Arrays, and the genome-wide genotyping data for 2.5 million markers using the Illumina Human Omni 2.5-Quad Bead Chips. In the second stage of this project, we provide whole-genome sequencing data, transcriptome data by mRNA-Seq, small RNA data by smRNA-seq, DNA cytosine methylation by Infinium HumanMethylation450 BeadChip, and epigenomic/epigenetic data by ChIP-Seq for H3K4me3, H3K27me3, H3K27ac and CTCF.
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Keywords
Versions (1)
- 12/6/22 12/6/22 - Simon Heim
Copyright Holder
Nenad Sestan, MD, PhD, Yale University, New Haven, CT, USA
Uploaded on
December 6, 2022
DOI
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License
Creative Commons BY 4.0
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dbGaP phs000755 BrainSpan Atlas of the Human Brain
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- This sample GEO mapping data table includes a mapping of study sample IDs to NCBI Gene Expression Omnibus (GEO) acccesions, type of GEO experiment, brain region, and left or right hemisphere.
- This sample attributes table includes body site where sample was collected and analyte type.
- The subject consent data table contains subject IDs, consent group information, and subject aliases.
- The subject sample mapping file includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases, and the substudy (phs accession) that the sample belongs to and sample use technology. The substudies are: Spatiotemporal Transcriptome of the Human Brain and BrainSpan Atlas of the Developing and Adult Human Brain.
- The dataset provides age (post conception days), sex, and ethnicity information of subjects whose post mortem brains were sampled.
- This sample attributes table includes body site where sample was collected and analyte type.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- This sample GEO mapping data table includes a mapping of study sample IDs to NCBI Gene Expression Omnibus (GEO) acccesions, type of GEO experiment, brain region, and left or right hemisphere.
- This sample attributes table includes body site where sample was collected and analyte type.
- The subject consent data table contains subject IDs, consent group information, and subject aliases.
- The subject sample mapping file includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases, and the substudy (phs accession) that the sample belongs to and sample use technology. The substudies are: Spatiotemporal Transcriptome of the Human Brain and BrainSpan Atlas of the Developing and Adult Human Brain.
- The dataset provides age (post conception days), sex, and ethnicity information of subjects whose post mortem brains were sampled.
- This sample attributes table includes body site where sample was collected and analyte type.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
C0680251 (UMLS CUI [1,2])
All selected subjects are normal according to following criteria:
Item
All selected subjects are normal according to following criteria:
boolean
C0681850 (UMLS CUI [1,1])
C0205307 (UMLS CUI [1,2])
C0205307 (UMLS CUI [1,2])
Subjects with chromosomal or large-scale genomic abnormalities, detected by karyogram and/or Illumina Human Omni-2.5, were excluded.
Item
Subjects with chromosomal or large-scale genomic abnormalities, detected by karyogram and/or Illumina Human Omni-2.5, were excluded.
boolean
C1706256 (UMLS CUI [1,1])
C0008625 (UMLS CUI [1,2])
C1517478 (UMLS CUI [1,3])
C0022526 (UMLS CUI [1,4])
C4687476 (UMLS CUI [1,5])
C0680251 (UMLS CUI [1,6])
C0008625 (UMLS CUI [1,2])
C1517478 (UMLS CUI [1,3])
C0022526 (UMLS CUI [1,4])
C4687476 (UMLS CUI [1,5])
C0680251 (UMLS CUI [1,6])
Prenatal and neonatal specimens were excluded if drug or alcohol abuse by the mother during pregnancy was reported or if potassium chloride, salt water, or urea were injected into the amniotic sac during surgical procedure.
Item
Prenatal and neonatal specimens were excluded if drug or alcohol abuse by the mother during pregnancy was reported or if potassium chloride, salt water, or urea were injected into the amniotic sac during surgical procedure.
boolean
C3669352 (UMLS CUI [1,1])
C0030761 (UMLS CUI [1,2])
C2828394 (UMLS CUI [1,3])
C2939425 (UMLS CUI [1,4])
C0370003 (UMLS CUI [1,5])
C0013146 (UMLS CUI [1,6])
C2215686 (UMLS CUI [1,7])
C0032825 (UMLS CUI [1,8])
C0337055 (UMLS CUI [1,9])
C0041942 (UMLS CUI [1,10])
C1533685 (UMLS CUI [1,11])
C0883994 (UMLS CUI [1,12])
C0543467 (UMLS CUI [1,13])
C0030761 (UMLS CUI [1,2])
C2828394 (UMLS CUI [1,3])
C2939425 (UMLS CUI [1,4])
C0370003 (UMLS CUI [1,5])
C0013146 (UMLS CUI [1,6])
C2215686 (UMLS CUI [1,7])
C0032825 (UMLS CUI [1,8])
C0337055 (UMLS CUI [1,9])
C0041942 (UMLS CUI [1,10])
C1533685 (UMLS CUI [1,11])
C0883994 (UMLS CUI [1,12])
C0543467 (UMLS CUI [1,13])
Only brains free of obvious malformations or lesions were collected. Disqualifying characteristics included any obvious abnormality of the neural tube, forebrain, brainstem, cranial nerves, cerebellum, or spinal cord.
Item
Only brains free of obvious malformations or lesions were collected. Disqualifying characteristics included any obvious abnormality of the neural tube, forebrain, brainstem, cranial nerves, cerebellum, or spinal cord.
boolean
C1838626 (UMLS CUI [1,1])
C0332197 (UMLS CUI [1,2])
C0332196 (UMLS CUI [1,3])
C1521970 (UMLS CUI [1,4])
C0231024 (UMLS CUI [1,5])
C0085140 (UMLS CUI [1,6])
C0006121 (UMLS CUI [1,7])
C0010268 (UMLS CUI [1,8])
C0007765 (UMLS CUI [1,9])
C0037925 (UMLS CUI [1,10])
C0332197 (UMLS CUI [1,2])
C0332196 (UMLS CUI [1,3])
C1521970 (UMLS CUI [1,4])
C0231024 (UMLS CUI [1,5])
C0085140 (UMLS CUI [1,6])
C0006121 (UMLS CUI [1,7])
C0010268 (UMLS CUI [1,8])
C0007765 (UMLS CUI [1,9])
C0037925 (UMLS CUI [1,10])
Samples were excluded if microscopic analysis revealed extensive neuronal loss, neuronal swelling, glioneuronal heterotopias, or dysmorphic neurons and neurites.
Item
Samples were excluded if microscopic analysis revealed extensive neuronal loss, neuronal swelling, glioneuronal heterotopias, or dysmorphic neurons and neurites.
boolean
C0370003 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
C0205288 (UMLS CUI [1,3])
C0936012 (UMLS CUI [1,4])
C0205231 (UMLS CUI [1,5])
C1850496 (UMLS CUI [1,6])
C3670503 (UMLS CUI [1,7])
C5563532 (UMLS CUI [1,8])
C5194942 (UMLS CUI [1,9])
C0085103 (UMLS CUI [1,10])
C0680251 (UMLS CUI [1,2])
C0205288 (UMLS CUI [1,3])
C0936012 (UMLS CUI [1,4])
C0205231 (UMLS CUI [1,5])
C1850496 (UMLS CUI [1,6])
C3670503 (UMLS CUI [1,7])
C5563532 (UMLS CUI [1,8])
C5194942 (UMLS CUI [1,9])
C0085103 (UMLS CUI [1,10])
Samples that tested positive for Hepatitis B, Hepatitis C, or HIV were excluded.
Item
Samples that tested positive for Hepatitis B, Hepatitis C, or HIV were excluded.
boolean
C0680251 (UMLS CUI [1,1])
C0019682 (UMLS CUI [1,2])
C0019163 (UMLS CUI [1,3])
C0019196 (UMLS CUI [1,4])
C0456984 (UMLS CUI [1,5])
C1446409 (UMLS CUI [1,6])
C0019682 (UMLS CUI [1,2])
C0019163 (UMLS CUI [1,3])
C0019196 (UMLS CUI [1,4])
C0456984 (UMLS CUI [1,5])
C1446409 (UMLS CUI [1,6])
Early postnatal and adult (periods 8-15) specimens were excluded if excessive drug or alcohol abuse was reported, if the individual had any known neurological or psychiatric disorders, or if any prolonged agonal conditions were reported.
Item
Early postnatal and adult (periods 8-15) specimens were excluded if excessive drug or alcohol abuse was reported, if the individual had any known neurological or psychiatric disorders, or if any prolonged agonal conditions were reported.
boolean
C0680251 (UMLS CUI [1,1])
C1279919 (UMLS CUI [1,2])
C0871109 (UMLS CUI [1,3])
C0001675 (UMLS CUI [1,4])
C0370003 (UMLS CUI [1,5])
C0013146 (UMLS CUI [1,6])
C0085762 (UMLS CUI [1,7])
C0700287 (UMLS CUI [1,8])
C0027765 (UMLS CUI [1,9])
C0004936 (UMLS CUI [1,10])
C0439590 (UMLS CUI [1,11])
C0521992 (UMLS CUI [1,12])
C1279919 (UMLS CUI [1,2])
C0871109 (UMLS CUI [1,3])
C0001675 (UMLS CUI [1,4])
C0370003 (UMLS CUI [1,5])
C0013146 (UMLS CUI [1,6])
C0085762 (UMLS CUI [1,7])
C0700287 (UMLS CUI [1,8])
C0027765 (UMLS CUI [1,9])
C0004936 (UMLS CUI [1,10])
C0439590 (UMLS CUI [1,11])
C0521992 (UMLS CUI [1,12])