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Sample GSM3536862 Query DataSets for GSM3536862
Status Public on Jan 02, 2019
Title APS_NEU_2
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: M
age: 67
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 0.324592637891581
cg00000108 0.906078628582121
cg00000109 0.789287704276313
cg00000165 0.150260704258627
cg00000236 0.541922366579201
cg00000289 0.52435807140896
cg00000292 0.710488739061567
cg00000321 0.249994493305433
cg00000363 0.253284764476348
cg00000622 0.0344278874424083
cg00000658 0.696952434276488
cg00000714 0.119980954288535
cg00000721 0.866800576716903
cg00000734 0.0651254519822977
cg00000769 0.114118745308784
cg00000807 0.775981313352206
cg00000884 0.792743582263711
cg00000905 0.0586375754234697
cg00000924 0.398783007822522
cg00000948 0.766156635699629

Total number of rows: 485512

Table truncated, full table size 13850 Kbytes.




Supplementary file Size Download File type/resource
GSM3536862_3999543043_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM3536862_3999543043_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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