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Series GSE59457 Query DataSets for GSE59457
Status Public on Jun 09, 2015
Title DNA methylation levels of various brain regions from HIV+ and HIV- subjects
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Genome wide DNA methylation profiles of various human brain regions (cerebellum, occipital lobe, etc). The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. The dataset includes 130 samples. Multiple brain regions were assessed per subject. The goal was to evaluate the effect of HIV infection on DNA methylation levels.
Genome wide DNA methylation profiles of various brain regions from HIV positive and negative subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 130 samples: 99 samples from HIV+ subjects and 31 samples from HIV- subjects.
 
Overall design The Illumina Infinium450 platform was applied to various brain regions from HIV+ and HIV- subjects. We evaluated 130 brain samples from 84 different subjects. Specifically, we considered cerebellum (20 HIV+ samples and 4 controls), frontal lobe (2 cases, 4 controls), hippocampus (4 controls), medial frontal cortex (18 cases), occipital cortex (59 cases, 13 controls), temporal cortex (4 controls). In total, there were 99 samples from HIV+ subjects and 31 samples from HIV- controls of similar ages. The subjects were recruited from the National Neurological AIDS Bank study or Multicenter AIDS Cohort study in Los Angeles. Informed consent and all study procedures were approved by the UCLA Medical IRB. DNAm data from HIV+ cases and HIV- controls were generated at the same time and randomized across plates and chips. HIV viral load information was available for blood (measured at the last blood draw) and for cerebrospinal fluid (CSF).
 
Contributor(s) Horvath S, Levine AJ
Citation(s) 25969563
Submission date Jul 16, 2014
Last update date Mar 22, 2019
Contact name Steve Horvath
E-mail(s) shorvath@altoslabs.com
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (130)
GSM1438127 genomic DNA from Brain CRBM of subject 75
GSM1438128 genomic DNA from Brain CRBM of subject 49
GSM1438129 genomic DNA from Brain Occipital of subject 27
Relations
BioProject PRJNA255454

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE59457_Explanation_of_characteristic_variables2.txt.gz 1.0 Kb (ftp)(http) TXT
GSE59457_RAW.tar 183.1 Mb (http)(custom) TAR
GSE59457_signals.csv.gz 301.3 Mb (ftp)(http) CSV
Processed data included within Sample table
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