NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3536874 Query DataSets for GSM3536874
Status Public on Jan 02, 2019
Title CON_NEU_96
Sample type genomic
 
Source name Neutrophil DNA
Organism Homo sapiens
Characteristics cell type: Neutrophil
disease status: healthy
Sex: M
age: 67
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 0.322840273229623
cg00000108 0.910434613587206
cg00000109 0.771431062465629
cg00000165 0.126091994740413
cg00000236 0.550393650712896
cg00000289 0.52395769700672
cg00000292 0.738099453455167
cg00000321 0.22819332280326
cg00000363 0.257674554819158
cg00000622 0.0528750424580127
cg00000658 0.711715170054045
cg00000714 0.108599319887917
cg00000721 0.866532040293986
cg00000734 0.0732288554692666
cg00000769 0.109249463570396
cg00000807 0.757479252874877
cg00000884 0.778813807563634
cg00000905 0.0650921763817358
cg00000924 0.4021677924891
cg00000948 0.761864774289247

Total number of rows: 485512

Table truncated, full table size 13851 Kbytes.




Supplementary file Size Download File type/resource
GSM3536874_3999543054_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM3536874_3999543054_R01C02_Red.idat.gz 4.1 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.