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Sample GSM3536872 Query DataSets for GSM3536872
Status Public on Jan 02, 2019
Title CON_NEU_88
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: F
age: 26
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 0.332170507053459
cg00000108 0.923960329678385
cg00000109 0.777316545774062
cg00000165 0.114419306184012
cg00000236 0.524930264993027
cg00000289 0.595086309378976
cg00000292 0.710239818253755
cg00000321 0.23907854837132
cg00000363 0.278188523717172
cg00000622 0.048532722689399
cg00000658 0.685757338797596
cg00000714 0.127772130456938
cg00000721 0.84445324138848
cg00000734 0.0675838467853937
cg00000769 0.113656996698832
cg00000807 0.778399626092063
cg00000884 0.796556320664148
cg00000905 0.0641664608186455
cg00000924 0.383808805895762
cg00000948 0.768796565337664

Total number of rows: 485512

Table truncated, full table size 13847 Kbytes.




Supplementary file Size Download File type/resource
GSM3536872_3999543054_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536872_3999543054_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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