|
Status |
Public on Nov 24, 2013 |
Title |
MS2946 |
Sample type |
genomic |
|
|
Source name |
Multiple sclerosis
|
Organism |
Homo sapiens |
Characteristics |
age: 59 years disease status: Multiple sclerosis tissue: Frontal lobe white matter gender: Male ms subtype: Primary Progressive ms duration: 12 years post mortem interval: 15 hours additional diagnosis: dementia
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Total DNA was isolated by phenol-chloroform extraction and ethanol precipitation
|
Label |
Cy3, Cy5
|
Label protocol |
Standard Illumina labelling protocol
|
|
|
Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
Scan protocol |
Arrays were imaged using standard recommended Illumina scanner protocol
|
Description |
none
|
Data processing |
GenomeStudio v2011.1 and Methylation module (within GenomeStudio) v1.9 was used to generate RAW_nonorm_nobg.txt and GenomeStudio_norm_bg.txt (linked as supplementary files on Series record). GenomeStudio's default parameters were used. GenomeStudio_norm_bg.txt AVG_Beta values were then quantile normalized to minimize batch effect (as the samples were run on different arrays). The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately. The quantile normalized Beta values form the basis of the study's conclusions.
|
|
|
Submission date |
Aug 24, 2012 |
Last update date |
Feb 25, 2014 |
Contact name |
Patrizia Casaccia |
E-mail(s) |
pcasaccia@gc.cuny.edu
|
Organization name |
ASRC-CUNY
|
Department |
Neuroscience
|
Street address |
85 St Nicholas Terrace
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10031 |
Country |
USA |
|
|
Platform ID |
GPL13534 |
Series (1) |
GSE40360 |
DNA methylation differences between multiple sclerosis and controls in frontal lobe white matter |
|