|
| Status |
Public on Oct 25, 2012 |
| Title |
A3-1 mRNA microarray - siGFP rep2 |
| Sample type |
RNA |
| |
|
| Source name |
cultured mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
sirna sequence: UGAAUUAGAUGGCGAUGUUdTdT/GACAUCGCCAUCUAAUUCAdTdT
cell line: A3-1
|
| Treatment protocol |
Mouse embryonic stem cell were treated with siRNA for GFP or for Lin28a and incubated for 48 hours.
|
| Growth protocol |
Mouse embryonic stem cell were incubated in DMEM media containing 20% FBS, non-essentail amino acid and LIF at 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified with Trizol reagent (Invitrogen) according to manufacturer's protocol
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Wt sensetarget label manual, 2007, Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human gene 1.0 ST arrays for 17 hr at 45˚C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G
|
| Description |
A3-1 treated with control siRNA
|
| Data processing |
All gene array data was analyzed using tools in Expression Console software (Affymetrix). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (gene-level) intensity analysis.
|
| |
|
| Submission date |
Apr 09, 2012 |
| Last update date |
Oct 25, 2012 |
| Contact name |
Hyeshik Chang |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University
|
| Department |
School of Biological Sciences
|
| Lab |
Hyeshik Chang Lab
|
| Street address |
Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| State/province |
South Korea |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE37113 |
Transcriptome profiling for changes upon Lin28a knockdown in mouse embryonic stem cell (A3-1) [Affymetrix] |
| GSE37114 |
LIN28A targets, regulation of microRNA biogenesis, and effect on transcriptome in A3-1 cells |
|
