|
| Status |
Public on Aug 24, 2009 |
| Title |
pKLO beta-catenin shRNA,, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured MM1S cell line, treated (maternal transcripts)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Multiple myeloma line MM1.S
protocol: beta-catenin knockdown
|
| Treatment protocol |
5x10^6 MM1.S cells lentivirally infected with control shRNA or beta-catenin shRNA vectors and sorted for GFP positive populations were cultured in triplicate, washed in PBS and then resuspended in Trizol reagent (invitrogen).
|
| Growth protocol |
Cell were grown and maintained in a 37oC incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to the manufacturer's protocol, purified using RNeasy kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Data were further process by the PLIER method.
|
| |
|
| Submission date |
Jul 28, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Daniel Ruben Carrasco |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Carrasco
|
| Street address |
44 Binney St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
MA 02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE17385 |
Gene expression profiling from MM1.S cells with control or beta-catenin knockdown. |
|
| Relations |
| Reanalyzed by |
GSE119087 |
