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Sample GSM4222590 Query DataSets for GSM4222590
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
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

Data table header descriptions
VALUE Average Beta

Data table
cg18478105 0.0255641470727474 0
cg09835024 0.0300181349622984 0
cg14361672 0.85692169803634 0
cg01763666 0.861952101220063 0
cg12950382 0.974127998324081 0
cg02115394 0.106359223300971 0
cg25813447 0.163153162154061 0
cg07779434 0.0636134385422598 0
cg13417420 0.0679590263244851 0
cg12480843 0.0197948011456332 0
cg26724186 0.918346701351254 0
cg24133276 0.0460656113787566 0
cg00617867 0.931531972123732 0
cg13773083 0.362969526903953 0
cg17236668 0.958610437367968 0
cg19607165 0.143179480372963 0
cg11073926 0.0894861050907865 0
cg08770523 0.00913282496896613 0
cg08795713 0.911200807265389 2.34533972091407e-30
cg24040570 0.0173704064249209 0

Total number of rows: 866238

Table truncated, full table size 28449 Kbytes.

Supplementary file Size Download File type/resource
GSM4222590_Sample3_Grn.idat.gz 7.1 Mb (ftp)(http) IDAT
GSM4222590_Sample3_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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