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Sample GSM3536861 Query DataSets for GSM3536861
Status Public on Jan 02, 2019
Title APS_NEU_3
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: F
age: 40
Extracted molecule genomic DNA
Extraction protocol Peripheral blood samples were collected from each participant, and Ficoll density gradient centrifugation was used to isolate peripheral blood mononuclear cells (PBMCs). Neutrophils were further isolated from the granulocyte layer through sedimentation by mixing a dextran solution with the red blood cell layer. Red blood cells were lysed using a hypotonic solution leaving a neutrophil population with ~95% purity. DNA was extracted immediately from the neutrophils using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) then bisulfite converted for DNA methylation studies using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA) using the provided protocol and thermocycler settings recommended by Zymo for Illumina DNA methylation array samples included in the product literature.
Label Cy3 and Cy5
Label protocol standard Illumina protocol
 
Hybridization protocol standard Illumina protocol
Scan protocol standard Illumina protocol
Data processing The R software package minfi was used to perform quantile normalization and extract beta (β) values for each methylation site which represents the fraction of methylated cytosines at a given site.
 
Submission date Jan 02, 2019
Last update date Jan 02, 2019
Contact name Amr Sawalha
E-mail(s) asawalha@pitt.edu
Organization name University of Pittsburgh
Street address 4401 Penn Avenue
City Pittsburgh
State/province PA
ZIP/Postal code 15224
Country USA
 
Platform ID GPL13534
Series (1)
GSE124565 Genome-wide DNA methylation analysis in primary antiphospholipid syndrome neutrophils

Data table header descriptions
ID_REF
VALUE Average Beta or normalized Average Beta

Data table
ID_REF VALUE
cg00000029 0.377093588590258
cg00000108 0.912648329789423
cg00000109 0.828547713849226
cg00000165 0.106044339928088
cg00000236 0.6088137260259
cg00000289 0.657548580890183
cg00000292 0.726136684428594
cg00000321 0.204893523748769
cg00000363 0.305516704360592
cg00000622 0.0296669577949449
cg00000658 0.702968709343628
cg00000714 0.121775581162897
cg00000721 0.857559231959663
cg00000734 0.071631548509024
cg00000769 0.112807126869468
cg00000807 0.749122198154642
cg00000884 0.780133153906084
cg00000905 0.0573602036747339
cg00000924 0.39160050005851
cg00000948 0.758295350157101

Total number of rows: 485512

Table truncated, full table size 13848 Kbytes.




Supplementary file Size Download File type/resource
GSM3536861_3999543043_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536861_3999543043_R06C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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