|
Status |
Public on Jan 02, 2019 |
Title |
APS_NEU_9 |
Sample type |
genomic |
|
|
Source name |
Neutrophil DNA
|
Organism |
Homo sapiens |
Characteristics |
cell type: Neutrophil disease status: APS Sex: F age: 40
|
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 |
|