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Sample GSM3536879 Query DataSets for GSM3536879
Status Public on Jan 02, 2019
Title CON_NEU_94
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: F
age: 39
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 0.387289992695398
cg00000108 0.900735264148944
cg00000109 0.790210513484462
cg00000165 0.145534598497325
cg00000236 0.576878660511266
cg00000289 0.537642769732817
cg00000292 0.727934263270064
cg00000321 0.188449708938418
cg00000363 0.280668792906618
cg00000622 0.0505588272323663
cg00000658 0.710302939282176
cg00000714 0.137835404224258
cg00000721 0.865914420626497
cg00000734 0.0693867179469499
cg00000769 0.113307240185176
cg00000807 0.760827877983753
cg00000884 0.794720368511191
cg00000905 0.0496589656875784
cg00000924 0.396743805015841
cg00000948 0.78420619972737

Total number of rows: 485512

Table truncated, full table size 13847 Kbytes.




Supplementary file Size Download File type/resource
GSM3536879_3999543054_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536879_3999543054_R06C02_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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