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Sample GSM3536863 Query DataSets for GSM3536863
Status Public on Jan 02, 2019
Title APS_NEU_9
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 0.303236074776153
cg00000108 0.887230771113132
cg00000109 0.814066750406498
cg00000165 0.129590285694545
cg00000236 0.550956995893858
cg00000289 0.602653423199716
cg00000292 0.72250247841321
cg00000321 0.217992125381092
cg00000363 0.229465858651785
cg00000622 0.0511603422223988
cg00000658 0.729101647783421
cg00000714 0.139621359869188
cg00000721 0.849485983092206
cg00000734 0.0775793313199201
cg00000769 0.119263035699326
cg00000807 0.71807508266509
cg00000884 0.79228129566327
cg00000905 0.064226827601913
cg00000924 0.375718959568769
cg00000948 0.767433917098563

Total number of rows: 485512

Table truncated, full table size 13848 Kbytes.




Supplementary file Size Download File type/resource
GSM3536863_3999543043_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536863_3999543043_R02C02_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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