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Sample GSM564448 Query DataSets for GSM564448
Status Public on Aug 11, 2010
Title shCDX2-2b
Sample type RNA
 
Source name CDX2 knockdown in Caco-2 cells
Organism Homo sapiens
Characteristics cell type: colon cancer cell line
cell line: Caco-2
Treatment protocol Cells were treated with lentivirus containing shCDX2 (MISSION TRCN13684 or shGFP (control)) when about 25% confluent and selected in 2ug/ml Puromycin until 1 day post confluent. Cells at this state are a heterogeneous population of dividing and differentiated CaCo2 cells.
Growth protocol Caco-2 cells were grown in 10% FBS DMEM and grown until 1 day post confluent on 6 well plates
Extracted molecule total RNA
Extraction protocol Trizol was used to extract RNA according to manufacturer's instructions
Label biotin
Label protocol Labeling, hybridization and scanning were done according to Affymetrix protocols
 
Hybridization protocol Labeling, hybridization and scanning were done according to Affymetrix protocols
Scan protocol Labeling, hybridization and scanning were done according to Affymetrix protocols
Data processing Data were processed using dChip 2006 software using default Affymetrix normalization settings.
The results file of comparison of shCDX2/shGFP contains dChip processed data with less stringent cutoffs to allow for larger selection of potentially regulated targets and is provided as a supplementary file on the Series record.
 
Submission date Jul 08, 2010
Last update date Aug 11, 2010
Contact name Michael P Verzi
Organization name Rutgers, the State University of New Jersey
Department Genetics
Lab Verzi
Street address 145 Bevier Road
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
 
Platform ID GPL570
Series (1)
GSE22572 TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions

Data table header descriptions
ID_REF
VALUE dChip normalized signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 573.095
AFFX-BioB-M_at 731.14
AFFX-BioB-3_at 615.338
AFFX-BioC-5_at 500.71
AFFX-BioC-3_at 513.258
AFFX-BioDn-5_at 3562.17
AFFX-BioDn-3_at 6895.73
AFFX-CreX-5_at 13290.5
AFFX-CreX-3_at 11651.2
AFFX-DapX-5_at 49.0288
AFFX-DapX-M_at 26.0192
AFFX-DapX-3_at 5.63844
AFFX-LysX-5_at 25.0487
AFFX-LysX-M_at 12.3088
AFFX-LysX-3_at 19.1152
AFFX-PheX-5_at 14.1687
AFFX-PheX-M_at 12.9496
AFFX-PheX-3_at 80.8903
AFFX-ThrX-5_at 19.3964
AFFX-ThrX-M_at 5.63844

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM564448.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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