ID

45241

Description

Principal Investigator: Nenad Sestan, Yale University School of Medicine, New Haven, CT, USA MeSH: Growth and Development,Aging https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000406 Comprehensive knowledge about the spatiotemporal dynamics of the brain transcriptome is essential for a better understanding of neurodevelopment, sexual dimorphism, and evolution, as well as our increased susceptibility to certain brain disorders. We generated and analyzed genome-wide exon-level transcriptome data from 16 brain regions of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genome-wide genotyping of 2.5 million SNPs and assessed genome normality for all donors. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of human neurodevelopment.

Link

dbGaP study = phs000406

Keywords

Versions (2)
  1. 7/13/22 7/13/22 - Dr. Christian Niklas
  2. 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder

Nenad Sestan, Yale University School of Medicine, New Haven, CT, USA

Uploaded on

October 12, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000406 Spatiotemporal Transcriptome of the Human Brain

English

Eligibility Criteria

6 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

All selected subjects are normal according to following criteria:
Description

All selected subjects are normal according to following criteria

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0681850
UMLS CUI [1,3]
C0460094
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.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0008625
UMLS CUI [1,3]
C1704258
UMLS CUI [1,4]
C0887950
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

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0370003
UMLS CUI [1,3]
C0678804
UMLS CUI [1,4]
C2939425
UMLS CUI [1,5]
C0013146
UMLS CUI [1,6]
C0001948
UMLS CUI [1,7]
C0026591
UMLS CUI [1,8]
C0347984
UMLS CUI [1,9]
C0032961
UMLS CUI [2,1]
C0680251
UMLS CUI [2,2]
C0370003
UMLS CUI [2,3]
C0678804
UMLS CUI [2,4]
C2939425
UMLS CUI [2,5]
C1272883
UMLS CUI [2,6]
C0883994
UMLS CUI [2,7]
C0032825
UMLS CUI [2,8]
C0036082
UMLS CUI [2,9]
C0041942
UMLS CUI [2,10]
C0347984
UMLS CUI [2,11]
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.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C1704258
UMLS CUI [1,3]
C3714787
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.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C2678195
UMLS CUI [1,3]
C3670503
UMLS CUI [1,4]
C0266491
UMLS CUI [1,5]
C5194942
UMLS CUI [1,6]
C0432072
UMLS CUI [1,7]
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.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0019693
UMLS CUI [1,3]
C0019163
UMLS CUI [1,4]
C0019196
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.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0038586
UMLS CUI [1,3]
C0004936
UMLS CUI [1,4]
C0027765
UMLS CUI [1,5]
C0262926
UMLS CUI [1,6]
C0439590
UMLS CUI [1,7]
C0030193
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Similar models

Eligibility Criteria

6 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
All selected subjects are normal according to following criteria
Item
All selected subjects are normal according to following criteria:
boolean
C1512693 (UMLS CUI [1,1])
C0681850 (UMLS CUI [1,2])
C0460094 (UMLS CUI [1,3])
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
C0680251 (UMLS CUI [1,1])
C0008625 (UMLS CUI [1,2])
C1704258 (UMLS CUI [1,3])
C0887950 (UMLS CUI [1,4])
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
C0680251 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
C0678804 (UMLS CUI [1,3])
C2939425 (UMLS CUI [1,4])
C0013146 (UMLS CUI [1,5])
C0001948 (UMLS CUI [1,6])
C0026591 (UMLS CUI [1,7])
C0347984 (UMLS CUI [1,8])
C0032961 (UMLS CUI [1,9])
C0680251 (UMLS CUI [2,1])
C0370003 (UMLS CUI [2,2])
C0678804 (UMLS CUI [2,3])
C2939425 (UMLS CUI [2,4])
C1272883 (UMLS CUI [2,5])
C0883994 (UMLS CUI [2,6])
C0032825 (UMLS CUI [2,7])
C0036082 (UMLS CUI [2,8])
C0041942 (UMLS CUI [2,9])
C0347984 (UMLS CUI [2,10])
C0543467 (UMLS CUI [2,11])
Only brains free of obvious malformations or lesions were collected.
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
C0680251 (UMLS CUI [1,1])
C1704258 (UMLS CUI [1,2])
C3714787 (UMLS CUI [1,3])
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
C0680251 (UMLS CUI [1,1])
C2678195 (UMLS CUI [1,2])
C3670503 (UMLS CUI [1,3])
C0266491 (UMLS CUI [1,4])
C5194942 (UMLS CUI [1,5])
C0432072 (UMLS CUI [1,6])
C0085103 (UMLS CUI [1,7])
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])
C0019693 (UMLS CUI [1,2])
C0019163 (UMLS CUI [1,3])
C0019196 (UMLS CUI [1,4])
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])
C0038586 (UMLS CUI [1,2])
C0004936 (UMLS CUI [1,3])
C0027765 (UMLS CUI [1,4])
C0262926 (UMLS CUI [1,5])
C0439590 (UMLS CUI [1,6])
C0030193 (UMLS CUI [1,7])
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