|
| Status |
Public on Nov 05, 2010 |
| Title |
shBAP1 #1 cells, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS osteosarcoma cell line transfected with shBAP1 #1 construct
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
treatment: shBAP1 #1
|
| Treatment protocol |
Cells were transfected with either a non-targeting control (shControl) or BAP1 RNA interference (shBAP1) plasmid using Lipofectamine 2000 and were selected with puromycin containing medium. Then, the cells were synchronized at the G1/S border using a thymidine double block protocol.
|
| Growth protocol |
U2OS osteosarcoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using Trizol reagent (Invitrogen) and the RNeasy kit (QIAGEN) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The generation of cDNA and biotinylated cRNA were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).
|
| |
|
| Hybridization protocol |
The hybridizations to Human genome Hu133 plus 2.0 arrays (Affymetrix) were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).
|
| Scan protocol |
Probe arrays have been scanned using the Affymetrix® GeneChip® Scanner 3000.
|
| Data processing |
Gene expression levels from shControl and shRNAs were subjected to comparative analysis using the expression analysis software Flex Array V1.1 (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), Genome Quebec, Montreal, Canada, URL http://genomequebec.mcgill.ca/FlexArray). Data were normalized with Robust Multi-Array Average (RMA) and the algorithm EB (Wright and Simon) was used for statistical analysis.
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| |
|
| Submission date |
Jul 20, 2010 |
| Last update date |
Nov 05, 2010 |
| Contact name |
El Bachir Affar |
| E-mail(s) |
el.bachir.affar@umontreal.ca
|
| Organization name |
Maisonneuve-Rosemont Hospital, University of Montreal
|
| Street address |
5415 boul. De l'Assomption
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T 2M4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE23035 |
Expression data from BAP1 depleted cells |
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