NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3536878 Query DataSets for GSM3536878
Status Public on Jan 02, 2019
Title CON_NEU_90
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: M
age: 57
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 0.372031070485328
cg00000108 0.908647959976384
cg00000109 0.788597548654129
cg00000165 0.0993942886493326
cg00000236 0.575904099409652
cg00000289 0.582886948367813
cg00000292 0.741740054536318
cg00000321 0.192431061328223
cg00000363 0.320487851921061
cg00000622 0.0507080776636136
cg00000658 0.71258557360245
cg00000714 0.116132528728602
cg00000721 0.881567953954697
cg00000734 0.0631848834380322
cg00000769 0.0988220008163782
cg00000807 0.745691652972654
cg00000884 0.805299479166667
cg00000905 0.0390053071380288
cg00000924 0.413978386876251
cg00000948 0.786613071828864

Total number of rows: 485512

Table truncated, full table size 13848 Kbytes.




Supplementary file Size Download File type/resource
GSM3536878_3999543054_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3536878_3999543054_R05C02_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.