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.

Lien

dbGaP study = phs000755

Mots-clés

Versions (1)
  1. 06/12/2022 06/12/2022 - Simon Heim
Détendeur de droits

Nenad Sestan, MD, PhD, Yale University, New Haven, CT, USA

Téléchargé le

6 décembre 2022

DOI

Pour une demande vous connecter.

Licence

Creative Commons BY 4.0
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dbGaP phs000755 BrainSpan Atlas of the Human Brain

Anglais

Eligibility Criteria

7 Formulaires  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
All selected subjects are normal according to following criteria:
Description

All selected subjects are normal according to following criteria:

Type de données

boolean

Alias
UMLS CUI [1,1]
C0681850
UMLS CUI [1,2]
C0205307
Subjects with chromosomal or large-scale genomic abnormalities, detected by karyogram and/or Illumina Human Omni-2.5, were excluded.
Description

Subjects with chromosomal or large-scale genomic abnormalities, detected by karyogram and/or Illumina Human Omni-2.5, were excluded.

Type de données

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C0008625
UMLS CUI [1,3]
C1517478
UMLS CUI [1,4]
C0022526
UMLS CUI [1,5]
C4687476
UMLS CUI [1,6]
C0680251
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.
Description

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.

Type de données

boolean

Alias
UMLS CUI [1,1]
C3669352
UMLS CUI [1,2]
C0030761
UMLS CUI [1,3]
C2828394
UMLS CUI [1,4]
C2939425
UMLS CUI [1,5]
C0370003
UMLS CUI [1,6]
C0013146
UMLS CUI [1,7]
C2215686
UMLS CUI [1,8]
C0032825
UMLS CUI [1,9]
C0337055
UMLS CUI [1,10]
C0041942
UMLS CUI [1,11]
C1533685
UMLS CUI [1,12]
C0883994
UMLS CUI [1,13]
C0543467
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.
Description

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.

Type de données

boolean

Alias
UMLS CUI [1,1]
C1838626
UMLS CUI [1,2]
C0332197
UMLS CUI [1,3]
C0332196
UMLS CUI [1,4]
C1521970
UMLS CUI [1,5]
C0231024
UMLS CUI [1,6]
C0085140
UMLS CUI [1,7]
C0006121
UMLS CUI [1,8]
C0010268
UMLS CUI [1,9]
C0007765
UMLS CUI [1,10]
C0037925
Samples were excluded if microscopic analysis revealed extensive neuronal loss, neuronal swelling, glioneuronal heterotopias, or dysmorphic neurons and neurites.
Description

Samples were excluded if microscopic analysis revealed extensive neuronal loss, neuronal swelling, glioneuronal heterotopias, or dysmorphic neurons and neurites.

Type de données

boolean

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0680251
UMLS CUI [1,3]
C0205288
UMLS CUI [1,4]
C0936012
UMLS CUI [1,5]
C0205231
UMLS CUI [1,6]
C1850496
UMLS CUI [1,7]
C3670503
UMLS CUI [1,8]
C5563532
UMLS CUI [1,9]
C5194942
UMLS CUI [1,10]
C0085103
Samples that tested positive for Hepatitis B, Hepatitis C, or HIV were excluded.
Description

Samples that tested positive for Hepatitis B, Hepatitis C, or HIV were excluded.

Type de données

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0019682
UMLS CUI [1,3]
C0019163
UMLS CUI [1,4]
C0019196
UMLS CUI [1,5]
C0456984
UMLS CUI [1,6]
C1446409
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.
Description

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.

Type de données

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C1279919
UMLS CUI [1,3]
C0871109
UMLS CUI [1,4]
C0001675
UMLS CUI [1,5]
C0370003
UMLS CUI [1,6]
C0013146
UMLS CUI [1,7]
C0085762
UMLS CUI [1,8]
C0700287
UMLS CUI [1,9]
C0027765
UMLS CUI [1,10]
C0004936
UMLS CUI [1,11]
C0439590
UMLS CUI [1,12]
C0521992
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Similar models

Eligibility Criteria

7 Formulaires
Name
Type
Description | Question | Decode (Coded Value)
Type de données
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
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])
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])
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])
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])
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])
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])
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])
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