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Sample GSM568513 Query DataSets for GSM568513
Status Public on Nov 05, 2010
Title shBAP1 #2 cells, rep3
Sample type RNA
 
Source name U2OS osteosarcoma cell line transfected with shBAP1 #2 construct
Organism Homo sapiens
Characteristics cell line: U2OS
treatment: shBAP1 #2
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.
 
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

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1557330_at 5.509581
241996_at 7.821062
1562934_at 3.772948
224644_at 9.194506
240617_at 6.196522
229849_at 4.949286
1563303_at 4.099936
244510_at 3.278256
228511_s_at 5.438093
234588_at 3.651008
1558515_at 6.336552
207779_at 3.204067
231608_at 4.566899
1557647_a_at 3.083911
1561089_at 4.073017
1554871_at 3.244106
229802_at 3.302124
241933_at 6.200596
209705_at 7.796699
244405_s_at 3.873446

Total number of rows: 54675

Table truncated, full table size 1051 Kbytes.




Supplementary file Size Download File type/resource
GSM568513_IG080812EAR009-2_01.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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