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Sample GSM3536870 Query DataSets for GSM3536870
Status Public on Jan 02, 2019
Title CON_NEU_84
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: F
age: 56
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 0.338288897264772
cg00000108 0.923978968678892
cg00000109 0.812325949145664
cg00000165 0.12524751461689
cg00000236 0.550811183804341
cg00000289 0.548659744023183
cg00000292 0.740101786899692
cg00000321 0.242525842343335
cg00000363 0.269590549293008
cg00000622 0.0669744622904245
cg00000658 0.671386160507748
cg00000714 0.129377662788877
cg00000721 0.864921564867472
cg00000734 0.060145173097966
cg00000769 0.0965600182591749
cg00000807 0.725944414174124
cg00000884 0.810385424014121
cg00000905 0.0588270632217637
cg00000924 0.398648057224152
cg00000948 0.792434166366379

Total number of rows: 485512

Table truncated, full table size 13845 Kbytes.




Supplementary file Size Download File type/resource
GSM3536870_3999543054_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536870_3999543054_R03C01_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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