ID

45452

Description

Principal Investigator: Graziano Pesole, Prof, IBIOM-CNR and University of Bari, Bari, Italy MeSH: Amyotrophic Lateral Sclerosis,Motor Neuron Disease,Neurodegenerative Diseases https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000747 Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is a fatal and devastating neurodegenerative disorder that causes the progressive death of upper and lower motor neurons. Although many efforts have been done to elucidate molecular factors involved in the onset and progression of the disorder, the causes of ALS are yet unknown and undefined. Transcriptome studies, based mostly on microarrays, have revealed multiple perturbations of the motor neuron function, supporting the current idea that several cellular events contribute to the pathobiology of the disease, including mitochondrial dysfunction, enhanced apoptosis, glutamate-mediated excitotoxicity, free radical injury, protein misfolding, abnormal calcium metabolism and altered axonal transport. In the present study, we have deeply sequenced the whole transcriptome of ventral horns of the human lumbar spinal cord from matched control and ALS post-mortem donors. Whole exome sequencing from the same donors has also been performed to exclude known genetic variants associated to the familiar form of ALS. In addition, to characterize the ALS transcriptome we have sequenced the RNA fraction at low molecular weight in the same tissues and individuals. Genomic and transcriptomic reads have been generated using the Illumina HiSeq2000 sequencer.

Link

dbGaP-study=phs000747

Keywords

Versions (1)
  1. 12/10/22 12/10/22 - Chiara Middel
Copyright Holder

Graziano Pesole, Prof, IBIOM-CNR and University of Bari, Bari, Italy

Uploaded on

December 10, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000747 Whole Exome and Transcriptome Sequencing in Sporadic ALS

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
We collected age- and sex- matched post-autopsy samples of ventral horns from lumbar spinal cord from 3 ALS and 3 controls. Samples were provided from NICHD Brain and Tissue Bank for Developmental Disorders (http://medschool.umaryland.edu/btbank/). Age was in the range 54-61 years old. Gender was male in all cases. Post-mortem delay was less than 10 hours for ALS samples. Race was Caucasian. ALS donor IDs (according to NICHD bank) were: 5388, 925 and 4762. Control donor IDs (according to NICHD bank) were: 5393, 5356 and 5362. Sample 5362 was identified as outlier based on our RNA-Seq experiments.
Description

Elig.phs000747.v2.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C0079399
UMLS CUI [1,3]
C0681880
UMLS CUI [1,4]
C0687676
UMLS CUI [1,5]
C0004398
UMLS CUI [1,6]
C0228590
UMLS CUI [1,7]
C0581621
UMLS CUI [1,8]
C0002736
UMLS CUI [1,9]
C0009932
UMLS CUI [2,1]
C0681880
UMLS CUI [2,2]
C0001779
UMLS CUI [3,1]
C0681880
UMLS CUI [3,2]
C0079399
UMLS CUI [3,3]
C0086582
UMLS CUI [4,1]
C0687676
UMLS CUI [4,2]
C1306577
UMLS CUI [4,3]
C1302413
UMLS CUI [4,4]
C0205421
UMLS CUI [4,5]
C0439092
UMLS CUI [4,6]
C0205456
UMLS CUI [4,7]
C0439227
UMLS CUI [5,1]
C0034510
UMLS CUI [5,2]
C0043157
UMLS CUI [6,1]
C0002736
UMLS CUI [6,2]
C1299222
UMLS CUI [7,1]
C0009932
UMLS CUI [7,2]
C1299222
We have extended the initial study collecting additional age- and sex- matched post-autopsy samples of ventral horns from lumbar spinal cord. Samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland - http://medschool.umaryland.edu/btbank/) and the Human Brain and Spinal Fluid Resource Center (Los Angeles, CA). Age was in the range 42-69 years old. Gender was male in all cases. Post-mortem delay was less than 19 hours and race was Caucasian. ALS donor IDs from NICHD bank were: 5595 and 1292. ALS donor IDs from HBSFRC bank were: 5215, 5187, 5165 and 5223. Control donor IDs from NICHD bank were: 5456, 5663, 5458, 5361 and 5617.
Description

Elig.phs000747.v2.p1.2

Data type

boolean

Alias
UMLS CUI [1,1]
C1524062
UMLS CUI [1,2]
C0079399
UMLS CUI [1,3]
C0001779
UMLS CUI [1,4]
C0681880
UMLS CUI [1,5]
C0687676
UMLS CUI [1,6]
C0004398
UMLS CUI [1,7]
C0228590
UMLS CUI [1,8]
C0581621
UMLS CUI [2,1]
C0001779
UMLS CUI [3,1]
C0079399
UMLS CUI [3,2]
C0086582
UMLS CUI [4,1]
C0687676
UMLS CUI [4,2]
C1306577
UMLS CUI [4,3]
C1302413
UMLS CUI [4,4]
C0205421
UMLS CUI [4,5]
C0439092
UMLS CUI [4,6]
C0450337
UMLS CUI [4,7]
C0439227
UMLS CUI [5,1]
C0034510
UMLS CUI [5,2]
C0043157
UMLS CUI [6,1]
C0002736
UMLS CUI [6,2]
C1299222
UMLS CUI [7,1]
C0009932
UMLS CUI [7,2]
C1299222
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Similar models

Eligibility Criteria

5 forms
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])
Elig.phs000747.v2.p1.1
Item
We collected age- and sex- matched post-autopsy samples of ventral horns from lumbar spinal cord from 3 ALS and 3 controls. Samples were provided from NICHD Brain and Tissue Bank for Developmental Disorders (http://medschool.umaryland.edu/btbank/). Age was in the range 54-61 years old. Gender was male in all cases. Post-mortem delay was less than 10 hours for ALS samples. Race was Caucasian. ALS donor IDs (according to NICHD bank) were: 5388, 925 and 4762. Control donor IDs (according to NICHD bank) were: 5393, 5356 and 5362. Sample 5362 was identified as outlier based on our RNA-Seq experiments.
boolean
C0001779 (UMLS CUI [1,1])
C0079399 (UMLS CUI [1,2])
C0681880 (UMLS CUI [1,3])
C0687676 (UMLS CUI [1,4])
C0004398 (UMLS CUI [1,5])
C0228590 (UMLS CUI [1,6])
C0581621 (UMLS CUI [1,7])
C0002736 (UMLS CUI [1,8])
C0009932 (UMLS CUI [1,9])
C0681880 (UMLS CUI [2,1])
C0001779 (UMLS CUI [2,2])
C0681880 (UMLS CUI [3,1])
C0079399 (UMLS CUI [3,2])
C0086582 (UMLS CUI [3,3])
C0687676 (UMLS CUI [4,1])
C1306577 (UMLS CUI [4,2])
C1302413 (UMLS CUI [4,3])
C0205421 (UMLS CUI [4,4])
C0439092 (UMLS CUI [4,5])
C0205456 (UMLS CUI [4,6])
C0439227 (UMLS CUI [4,7])
C0034510 (UMLS CUI [5,1])
C0043157 (UMLS CUI [5,2])
C0002736 (UMLS CUI [6,1])
C1299222 (UMLS CUI [6,2])
C0009932 (UMLS CUI [7,1])
C1299222 (UMLS CUI [7,2])
Elig.phs000747.v2.p1.2
Item
We have extended the initial study collecting additional age- and sex- matched post-autopsy samples of ventral horns from lumbar spinal cord. Samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland - http://medschool.umaryland.edu/btbank/) and the Human Brain and Spinal Fluid Resource Center (Los Angeles, CA). Age was in the range 42-69 years old. Gender was male in all cases. Post-mortem delay was less than 19 hours and race was Caucasian. ALS donor IDs from NICHD bank were: 5595 and 1292. ALS donor IDs from HBSFRC bank were: 5215, 5187, 5165 and 5223. Control donor IDs from NICHD bank were: 5456, 5663, 5458, 5361 and 5617.
boolean
C1524062 (UMLS CUI [1,1])
C0079399 (UMLS CUI [1,2])
C0001779 (UMLS CUI [1,3])
C0681880 (UMLS CUI [1,4])
C0687676 (UMLS CUI [1,5])
C0004398 (UMLS CUI [1,6])
C0228590 (UMLS CUI [1,7])
C0581621 (UMLS CUI [1,8])
C0001779 (UMLS CUI [2,1])
C0079399 (UMLS CUI [3,1])
C0086582 (UMLS CUI [3,2])
C0687676 (UMLS CUI [4,1])
C1306577 (UMLS CUI [4,2])
C1302413 (UMLS CUI [4,3])
C0205421 (UMLS CUI [4,4])
C0439092 (UMLS CUI [4,5])
C0450337 (UMLS CUI [4,6])
C0439227 (UMLS CUI [4,7])
C0034510 (UMLS CUI [5,1])
C0043157 (UMLS CUI [5,2])
C0002736 (UMLS CUI [6,1])
C1299222 (UMLS CUI [6,2])
C0009932 (UMLS CUI [7,1])
C1299222 (UMLS CUI [7,2])
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