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Sample GSM3536873 Query DataSets for GSM3536873
Status Public on Jan 02, 2019
Title CON_NEU_85
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: F
age: 40
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 0.332205491239897
cg00000108 0.923542605596898
cg00000109 0.813632713072226
cg00000165 0.117870927776101
cg00000236 0.609264978019432
cg00000289 0.589392138184051
cg00000292 0.754267683357626
cg00000321 0.248363154738105
cg00000363 0.263567699321427
cg00000622 0.0420689308176101
cg00000658 0.68786625615614
cg00000714 0.129574981599083
cg00000721 0.859812003772093
cg00000734 0.0651419002635318
cg00000769 0.106723468157355
cg00000807 0.759495972702087
cg00000884 0.782069584916789
cg00000905 0.0532901775436411
cg00000924 0.416318064113067
cg00000948 0.760016844511622

Total number of rows: 485512

Table truncated, full table size 13847 Kbytes.




Supplementary file Size Download File type/resource
GSM3536873_3999543054_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536873_3999543054_R06C01_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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