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Sample GSM3536868 Query DataSets for GSM3536868
Status Public on Jan 02, 2019
Title CON_NEU_86
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: F
age: 32
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 0.379998105980891
cg00000108 0.906683671920075
cg00000109 0.789331186365806
cg00000165 0.125375986411409
cg00000236 0.594841735052755
cg00000289 0.604416251806648
cg00000292 0.714543032874929
cg00000321 0.176319953875218
cg00000363 0.237938660973396
cg00000622 0.0420945188495204
cg00000658 0.695397412624371
cg00000714 0.11525241732155
cg00000721 0.892085033747844
cg00000734 0.0593192316556278
cg00000769 0.119916721202524
cg00000807 0.786389999091094
cg00000884 0.821648163810054
cg00000905 0.056872905031209
cg00000924 0.379811420514628
cg00000948 0.805536232093659

Total number of rows: 485512

Table truncated, full table size 13846 Kbytes.




Supplementary file Size Download File type/resource
GSM3536868_3999543054_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM3536868_3999543054_R01C01_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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