NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM568505 Query DataSets for GSM568505
Status Public on Nov 05, 2010
Title shControl cells, rep1
Sample type RNA
 
Source name U2OS osteosarcoma cell line transfected with an shControl construct
Organism Homo sapiens
Characteristics cell line: U2OS
treatment: shControl
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 5.693113
241996_at 7.91554
1562934_at 3.943401
224644_at 10.34047
240617_at 6.17643
229849_at 4.508119
1563303_at 4.121351
244510_at 3.252716
228511_s_at 5.200175
234588_at 3.628634
1558515_at 6.882728
207779_at 3.451746
231608_at 3.954974
1557647_a_at 3.063754
1561089_at 3.906326
1554871_at 3.244106
229802_at 3.497422
241933_at 5.903067
209705_at 7.411601
244405_s_at 3.569366

Total number of rows: 54675

Table truncated, full table size 1051 Kbytes.




Supplementary file Size Download File type/resource
GSM568505_IG080812EAR001-2_01.CEL.gz 4.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap