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Status |
Public on Dec 07, 2020 |
Title |
switched_mem_tripletB |
Sample type |
genomic |
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Source name |
switched memory B cells, triplet B, Hodgkins lymphoma
|
Organism |
Homo sapiens |
Characteristics |
disease state: Hodgkins lymphoma triplet: B cell population: switched memory 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.
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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
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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.
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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 |
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