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Sample GSM3536864 Query DataSets for GSM3536864
Status Public on Jan 02, 2019
Title APS_NEU_4
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: M
age: 61
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 0.297363054211695
cg00000108 0.902591978616498
cg00000109 0.79315786866335
cg00000165 0.135472984955891
cg00000236 0.515891755860376
cg00000289 0.593856573033031
cg00000292 0.75923932339578
cg00000321 0.200240035580206
cg00000363 0.26762580689771
cg00000622 0.028680617736382
cg00000658 0.718814876278742
cg00000714 0.119635365482885
cg00000721 0.88268639627643
cg00000734 0.06713240869969
cg00000769 0.131913881839967
cg00000807 0.770489492890399
cg00000884 0.8210970344077
cg00000905 0.053429810377144
cg00000924 0.37986041638582
cg00000948 0.771184660668506

Total number of rows: 485512

Table truncated, full table size 13851 Kbytes.




Supplementary file Size Download File type/resource
GSM3536864_3999543043_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536864_3999543043_R03C02_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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