NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3536867 Query DataSets for GSM3536867
Status Public on Jan 02, 2019
Title APS_NEU_10
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: APS
Sex: F
age: 42
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 0.34889306029849
cg00000108 0.917963980982539
cg00000109 0.766824577278615
cg00000165 0.137970760567268
cg00000236 0.599796267445281
cg00000289 0.532894661555187
cg00000292 0.721892490777247
cg00000321 0.218079827197889
cg00000363 0.280750199920032
cg00000622 0.0554717353330057
cg00000658 0.718271073171189
cg00000714 0.13335085827568
cg00000721 0.890034407892231
cg00000734 0.0680831179901129
cg00000769 0.118240808871307
cg00000807 0.776080466453822
cg00000884 0.790016638935108
cg00000905 0.0555589004932497
cg00000924 0.417355234013175
cg00000948 0.755372582248831

Total number of rows: 485512

Table truncated, full table size 13846 Kbytes.




Supplementary file Size Download File type/resource
GSM3536867_3999543043_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536867_3999543043_R06C02_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.