|
| Status |
Public on Nov 24, 2013 |
| Title |
MS097 |
| Sample type |
genomic |
| |
|
| Source name |
Multiple sclerosis
|
| Organism |
Homo sapiens |
| Characteristics |
age: 55 years
disease status: Multiple sclerosis
tissue: Frontal lobe white matter
gender: Male
ms subtype: Secondary Progressive
ms duration: 22 years
post mortem interval: 31 hours
additional diagnosis: bronchopneumonia
|
| 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 |
|
