|
| Status |
Public on Oct 01, 2016 |
| Title |
9974366111_R04C02 |
| Sample type |
genomic |
| |
|
| Source name |
Naïve CD4+ T cell
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy Control
cell type: CD4+ T cell
gender: Female
race: African-American
age: 35
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole blood was collected at the time of enrollment and processed within 6 h of collection. Peripheral blood mononuclear cells were isolated using Ficoll density gradient centrifugation media (GE Healthcare Biosciences, USA) followed by indirect isolation of untouched naïve CD4+ T cells using the Naïve CD4+ T cell Isolation Kit II (Miltenyi Biotec Inc., USA). DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen, USA) and DNA concentration was determined by spectrophotometry on the NanoDrop 2000 (Thermo Scientific, USA). Flow cytometry was used to confirm purity of isolated naïve CD4+ T cells using CD4 and CD45RA fluorochromeconjugated antibodies (BioLegend, USA).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Staining Protocol (Tecan Freedom Evo): XStain HD BeadChip
|
| |
|
| Hybridization protocol |
Hybridization: 22 hr at 48 degrees C. (full protocol details for all steps can be found in Illumina Infinium HD Methylation Assay manual)
|
| Scan protocol |
iScan Scan Setting: Methylation NXT
|
| Data processing |
β values are calculated using the formula: β = Methylated / (Methylated + Unmethylated + 100). The file methyl_and_unmethylated_signal_Annotated_AA_vs_EA.txt is available on the series record and contains the non-normalized beta values, detection p-values and raw methylated and unmethylated signal in addition to probe annotation.
|
| |
|
| Submission date |
Mar 15, 2016 |
| Last update date |
Oct 01, 2016 |
| Contact name |
Jonathan Daniel Wren |
| E-mail(s) |
[email protected]
|
| Organization name |
Oklahoma Medical Research Foundation
|
| Department |
Arthritis & Clinical Immunology
|
| Lab |
MC103
|
| Street address |
825 NE 13th St
|
| City |
OKC |
| State/province |
OK |
| ZIP/Postal code |
73104-5005 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE79237 |
Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity |
|
