|
| Status |
Public on Mar 29, 2015 |
| Title |
hESCs cultured on extacellular matrix and mechanically passaged P6 mRNA RepA |
| Sample type |
RNA |
| |
|
| Source name |
WA09
|
| Organism |
Homo sapiens |
| Characteristics |
growth condition: extacellular matrix and mechanically passagged P6
passage: P6
cell line: WA09
gender: female
|
| Growth protocol |
Human Embryonic Stem Cells grew in different subtrates (Feeder Layer and extracellular matrix) and were passaged with different methods (mechanically and enzymatically)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Biological Replicate A
|
| Data processing |
The data were filtered for detection pValue <= 0.05 and normalised using robust spline normalisation with lumi in R. Filtering in Genome Studio using the OR clause (it means that even only a sample has a p-value lower than 0.05 for one specific probe, this probe will be selected).
|
| |
|
| Submission date |
Jan 10, 2012 |
| Last update date |
Mar 29, 2015 |
| Contact name |
Francesca Boscolo |
| E-mail(s) |
francesca.boscolo@gmail.com
|
| Organization name |
UCSD
|
| Department |
Reproductive Medicine
|
| Lab |
Marianna Alperin
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL6884 |
| Series (2) |
| GSE34982 |
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions I |
| GSE56851 |
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions |
|
