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Sample GSM3536866 Query DataSets for GSM3536866
Status Public on Jan 02, 2019
Title APS_NEU_8
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: M
age: 52
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 0.332905028789218
cg00000108 0.879989926205457
cg00000109 0.773027747824981
cg00000165 0.122422949236794
cg00000236 0.61276868963207
cg00000289 0.503722970945106
cg00000292 0.770794345662518
cg00000321 0.225042719460607
cg00000363 0.26689009417152
cg00000622 0.0560896183245074
cg00000658 0.712596777724333
cg00000714 0.131174838112858
cg00000721 0.907267673985305
cg00000734 0.0671424053475686
cg00000769 0.128354978521506
cg00000807 0.742127857648162
cg00000884 0.826056703140776
cg00000905 0.063662910016301
cg00000924 0.402018836465234
cg00000948 0.767175307733375

Total number of rows: 485512

Table truncated, full table size 13850 Kbytes.




Supplementary file Size Download File type/resource
GSM3536866_3999543043_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536866_3999543043_R05C02_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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