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Sample GSM3536876 Query DataSets for GSM3536876
Status Public on Jan 02, 2019
Title CON_NEU_91
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: M
age: 59
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 0.343492588512132
cg00000108 0.883985062705691
cg00000109 0.776099998271122
cg00000165 0.106263766207225
cg00000236 0.567859858016297
cg00000289 0.578741227344691
cg00000292 0.754909041817139
cg00000321 0.247428827179709
cg00000363 0.308890408910267
cg00000622 0.057462768968155
cg00000658 0.726927215242257
cg00000714 0.113724429427959
cg00000721 0.872006750444505
cg00000734 0.0610403314659921
cg00000769 0.100523675454066
cg00000807 0.735570544211402
cg00000884 0.788681863869027
cg00000905 0.0684051941367589
cg00000924 0.37466305409844
cg00000948 0.792851699367331

Total number of rows: 485512

Table truncated, full table size 13850 Kbytes.




Supplementary file Size Download File type/resource
GSM3536876_3999543054_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536876_3999543054_R03C02_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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