NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3536859 Query DataSets for GSM3536859
Status Public on Jan 02, 2019
Title APS_NEU_5
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: M
age: 37
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 0.362291042795952
cg00000108 0.903810075084876
cg00000109 0.811631485473353
cg00000165 0.117008783878999
cg00000236 0.644389630371338
cg00000289 0.655799445052321
cg00000292 0.737510550219043
cg00000321 0.199766629165976
cg00000363 0.257638333349397
cg00000622 0.0471932860804823
cg00000658 0.703785072728718
cg00000714 0.122196726122977
cg00000721 0.851023101590279
cg00000734 0.0630338314123584
cg00000769 0.112392413760739
cg00000807 0.766474677940238
cg00000884 0.781127096576186
cg00000905 0.0684507877136431
cg00000924 0.424300830632526
cg00000948 0.802865159405071

Total number of rows: 485512

Table truncated, full table size 13852 Kbytes.




Supplementary file Size Download File type/resource
GSM3536859_3999543043_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536859_3999543043_R04C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.