|
| Status |
Public on Jan 18, 2013 |
| Title |
Syncytio 1% oxygen 100Vitd (methylation) 91 |
| Sample type |
genomic |
| |
|
| Source name |
cultured syncytiotrophoblast, 1% oxygen conditions, 100 nmvitamin D
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fused Cytotrophoblast cells (syncitiotrophoblast)
treatment: 1% oxygen conditions, 100 nm vitamin D
|
| Treatment protocol |
Half of the cells from each placenta were continued in standard conditions of 5% carbon dioxide/air for 48 h until exposure to <1% oxygen conditions (<1% O2/5%CO2/10%H2/balance N2), 8% oxygen conditions (8% O2/5%CO2/10%H2/balance N2) or standard conditions with or without active vitamin D (1α, 25-dihydroxyvitamin D3) (10 nM or 100 nM), while the other half of the cells were exposed to <1% oxygen, 8%, or standard conditions for 24 h with or without active vitamin D.
|
| Growth protocol |
Cultures were plated at a density of 300,000 cells/cm2 and maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum, 20 mmol/liter HEPES pH 7.4 , penicillin (100 units/ml), streptomycin (100 μg/ml), and fungizone (0.25 μg/ml) at 37°C in a 5% carbon dioxide/air atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from cultured trophoblasts using Wizard® Genomic DNA Purification Kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Illumina hiScan machine using standard Illumina Settings
|
| Data processing |
GenomeStudio- Background Subtraction. R- Colour Correction and Quantile Normalization using Methyllumi package
|
| |
|
| Submission date |
Oct 03, 2012 |
| Last update date |
May 17, 2016 |
| Contact name |
Wendy Robinson |
| E-mail(s) |
wprobinsonlab@gmail.com
|
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Robinosn
|
| Street address |
950 W 28th Ave
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE41336 |
Cultured Cyto and Syncytio-trophoblast samples exposed to varying degrees of hypoxia (methylation) |
| GSE41341 |
Cultured Cyto and Syncytio-trophoblast samples exposed to varying degrees of hypoxia |
|
