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Sample GSM3536865 Query DataSets for GSM3536865
Status Public on Jan 02, 2019
Title APS_NEU_6
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: M
age: 36
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 0.275208174922572
cg00000108 0.88975449464259
cg00000109 0.799261540268444
cg00000165 0.128662074167748
cg00000236 0.577259069878811
cg00000289 0.594280771011526
cg00000292 0.738376487145072
cg00000321 0.308434898574299
cg00000363 0.255308163923846
cg00000622 0.0601238537912177
cg00000658 0.711781294398876
cg00000714 0.124806142446237
cg00000721 0.86907736522302
cg00000734 0.0604540886144948
cg00000769 0.119999685576613
cg00000807 0.746017967764275
cg00000884 0.79349008912214
cg00000905 0.061884647252318
cg00000924 0.405386015258627
cg00000948 0.763898493446297

Total number of rows: 485512

Table truncated, full table size 13852 Kbytes.




Supplementary file Size Download File type/resource
GSM3536865_3999543043_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536865_3999543043_R04C02_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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