|
| Status |
Public on Sep 24, 2018 |
| Title |
Placental-Obese-BioRep8-TechRep1 |
| Sample type |
genomic |
| |
|
| Source name |
Placental-Obese
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
sample type: Placental tissue punch
weight: Obese
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from frozen tissue (Vanderbilt University Medical Center, Nashville, TN) using a DNeasy Blood and Tissue kit (Qiagen, Valencia, CA).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Obese frozen placental punch
|
| Data processing |
Data was processed with the R packages wateRmelon, methylumi, minfi, and Limma. Probes containing SNPs, a detection p-value of greater than 0.001 in more than 1% of the samples, or a beadcount of less than 3 in 5% of samples were removed. To correct for the differences in probe design, the BMIQ (Beta Mixture Quantile) normiization was used. The function “duplicateCorrelation” was used to account for samples that came from the same patient.
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Sep 25, 2018 |
| Contact name |
Kate J Claycombe-Larson |
| E-mail(s) |
Kate.Larson@ars.usda.gov
|
| Phone |
701-795-8298
|
| Organization name |
USDA
|
| Department |
ARS
|
| Lab |
Nutritional Immunology and Epigenetics
|
| Street address |
2420 2nd Avenue North
|
| City |
Grand Forks |
| State/province |
ND |
| ZIP/Postal code |
58203 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE120062 |
DNA Methylation data from frozen placental tissue |
|
