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Sample GSM3536858 Query DataSets for GSM3536858
Status Public on Jan 02, 2019
Title APS_NEU_1
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: F
age: 33
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 0.314126599454663
cg00000108 0.883788115180116
cg00000109 0.846710972659816
cg00000165 0.137749856022973
cg00000236 0.532852774023858
cg00000289 0.515318692459125
cg00000292 0.737265669979817
cg00000321 0.194004396644355
cg00000363 0.348587403292568
cg00000622 0.0422349519907771
cg00000658 0.713187919882902
cg00000714 0.117463359297325
cg00000721 0.855970756414223
cg00000734 0.0682280855819895
cg00000769 0.139070682955694
cg00000807 0.762936904625034
cg00000884 0.758771616102783
cg00000905 0.0550226975537672
cg00000924 0.386347258266317
cg00000948 0.770229696392438

Total number of rows: 485512

Table truncated, full table size 13848 Kbytes.




Supplementary file Size Download File type/resource
GSM3536858_3999543043_R01C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536858_3999543043_R01C01_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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