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Sample GSM3536871 Query DataSets for GSM3536871
Status Public on Jan 02, 2019
Title CON_NEU_81
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: M
age: 41
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 0.318663924344161
cg00000108 0.89767946633592
cg00000109 0.771652129680884
cg00000165 0.109009066641853
cg00000236 0.552573636647574
cg00000289 0.567886941092081
cg00000292 0.746695922394588
cg00000321 0.230004496417217
cg00000363 0.271043976278461
cg00000622 0.0507416830833221
cg00000658 0.721031351189689
cg00000714 0.130532833945747
cg00000721 0.876425787958828
cg00000734 0.0647387858785372
cg00000769 0.103062826438516
cg00000807 0.741661575752798
cg00000884 0.789526906086116
cg00000905 0.0501831556302388
cg00000924 0.406113702988703
cg00000948 0.779209257473481

Total number of rows: 485512

Table truncated, full table size 13851 Kbytes.




Supplementary file Size Download File type/resource
GSM3536871_3999543054_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536871_3999543054_R04C01_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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