|
| Status |
Public on Jun 17, 2015 |
| Title |
CD19+ cells CVID twin (replicate 1) |
| Sample type |
genomic |
| |
|
| Source name |
CD19+ cells CVID twin
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
subject: CVID twin
tissue: peripheral blood
cell type: CD19+ cells (B lymphocytes)
|
| Growth protocol |
Human B lymphocytes were isolated using MACS CD19 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Proteinase K extraction
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting
|
| Description |
CVID R1
|
| Data processing |
Data were extracted with Genome Studio V2011.2. Each methylation data point is obtained from a combination of the Cy3 and Cy5 fluorescent intensities from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each data point. For data processing, we transformed Beta values into M-values and used limma Bioconductor package for the differential methylation analysis. Given the following observations (1) technical variability was similar to biological variability, (2) many DNA methylation changes we expected to be mild, and (3) the reduced number of samples (1 twin pair) we made a conservative selection of probes as candidate differentially methylated sites: (i) 10% or greater difference in the Betavalue DNA methylation between MZ twins, (ii) p-value smaller than 0.01 and (iii) in the three replicates the Beta-value estimated of one twin were always larger or always smaller than the other twin.
The non_normalized.txt contains unmethylated and methylated signal intensities.
|
| |
|
| Submission date |
Dec 04, 2014 |
| Last update date |
Jun 17, 2015 |
| Contact name |
Esteban Ballestar |
| Organization name |
Josep Carreras Research Institute (IJC)
|
| Lab |
Epigenetics and Immune Disease
|
| Street address |
Ctra de Can Ruti, Camà de les Escoles s/n
|
| City |
Badalona, Barcelona |
| State/province |
N/A = Not Applicable |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE63849 |
Comparison of the DNA methylation profiles of CD19+ B lymphocytes of a pair of monozygotic twins discordant for common variable immunodeficiency |
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