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Sample GSM3536860 Query DataSets for GSM3536860
Status Public on Jan 02, 2019
Title APS_NEU_7
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: F
age: 28
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 0.362258258491261
cg00000108 0.912371706844683
cg00000109 0.817494668612156
cg00000165 0.126654612826179
cg00000236 0.585662191641072
cg00000289 0.614481241598436
cg00000292 0.724812010667114
cg00000321 0.252106130459738
cg00000363 0.268712155844218
cg00000622 0.0553527799117718
cg00000658 0.710188840060206
cg00000714 0.131929617967557
cg00000721 0.853903870613907
cg00000734 0.0661195107340525
cg00000769 0.113973295299718
cg00000807 0.753079978456981
cg00000884 0.758923710476722
cg00000905 0.0535104328217619
cg00000924 0.395918688668234
cg00000948 0.745037987606043

Total number of rows: 485512

Table truncated, full table size 13847 Kbytes.




Supplementary file Size Download File type/resource
GSM3536860_3999543043_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536860_3999543043_R05C01_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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