|
| Status |
Public on Dec 07, 2020 |
| Title |
marginal_zone_tripletA |
| Sample type |
genomic |
| |
|
| Source name |
marginal zone-like B cells, triplet A, Hodgkins lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Hodgkins lymphoma
triplet: A
cell population: marginal zone-like B cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from CD34+ cells and from Naïve, marginal zone-like and switched memory B cells using the Dneasy Blood & Tissue Kit (Qiagen) in accordance with the manufacturer's protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Bisulphite conversion was performed using the EZ DNA Methylation Kit from Zymo Research with 250 ng of DNA per sample.
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was eluted in 15 microliters according to the manufacturer's protocol, evaporated to a volume of <4 microliters, and used for methylation analysis using the Illumina Methylation EPIC array.
|
| Scan protocol |
Arrays were imaged using Illumina's iScan system
|
| Data processing |
Idat files were processed using minfi R package v1.28.4. Idat files were read with the read.metharray.exp function. Detection P values were generated using the detectionP function. Methylated and unmethylated signals were generated using the preprocessIllumina function with parameters bg.correct=TRUE and no normalization. Beta values were extracted using the getBeta function on methylated/unmethylated values.
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Klas Strååt |
| E-mail(s) |
klas.straat@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Medicine
|
| Lab |
Hematology lab
|
| Street address |
Akademiska stråket 1
|
| City |
Solna |
| ZIP/Postal code |
171 64 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23976 |
| Series (1) |
| GSE142202 |
Genome-wide methylation analysis of blood cells from homozygotic triplets |
|
