|
| Status |
Public on Jan 14, 2015 |
| Title |
Cordblood_200 |
| Sample type |
genomic |
| |
|
| Source name |
Cordblood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
race: AA
batch: 9
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Newborn umbilical cord blood was collected at delivery. Whole blood was centrifuged and buffy coat layer isolated and frozen until processed for nucleic acid purification. DNA extraction was performed with Wizard genomics DNA purification reagents (Promega; http://www.promega.com).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Humanmethylation27 array protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Humanmethylation27 array protocol
|
| Scan protocol |
Standard Illumina Humanmethylation27 array protocol
|
| Description |
Normal newbord cord blood
|
| Data processing |
Raw data was processed using the Illumina GenomeStudio (version 2009.1). Beta values with detection p-value ≥ 0.001 were considered as missing data. One probe with a median detection p-value ≥ 10-6 across all samples was dropped from analysis. The data was then corrected for batch effects using the COMBAT R package. Following the batch correction, the β values were converted to M-values using a logit transform.
|
| |
|
| Submission date |
Jan 13, 2015 |
| Last update date |
Jan 14, 2015 |
| Contact name |
Khyobeni Mozhui |
| E-mail(s) |
kmozhui@uthsc.edu
|
| Organization name |
University of Tennessee Health Science Center
|
| Department |
Preventive Medicine
|
| Street address |
66 N. Pauline Street, #631
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38163 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE64940 |
DNA methylation in newborn cordblood |
|
