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Sample GSM112330 Query DataSets for GSM112330
Status Public on Jun 06, 2006
Title SCC-6 cells transfected with p63 siRNA
Sample type RNA
Source name SCC-6 cells transfected with vector expressing p63 siRNA
Organism Homo sapiens
Characteristics head and neck squamous cell carcinoma

Treatment protocol Cells were transfected using Fugene 6 (Roche, Indianapolis, IN). Cells were selected with hygromycin B 48 h after transfection and harvested for mRNA isolation.
Growth protocol Cells were grown in DMEM+10% FBS at 37C and harvested for mRNA after selection with Hygromycin
Extracted molecule polyA RNA
Extraction protocol mRNA isolation was performed as described in Flatt, P. M., Tang, L. J., Scatena, C. D., Szak, S. T., and Pietenpol, J. A. (2000) Mol Cell Biol 20, 4210-4223
Label biotin
Label protocol 300 ng of mRNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
Hybridization protocol biotinylated cRNA (15µg) was fragmented and hybridized to the Affymetrix GeneChip U133 Plus 2.0. Hybridized cRNAs were washed and detected via streptavidin coupled to phycoerythrin using the Affymetrix 450 Fluidics Station and recommended protocols.
Scan protocol Results were visualized by laser scanner (Affymetrix GeneChip Scanner 3000).
Description Gene expression data on Affy HG133 Plus 2.0 from SCC-6 cells transfected with p63 siRNA
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.
Submission date Jun 05, 2006
Last update date Jun 05, 2006
Contact name Jennifer Pietenpol
Organization name Vanderbilt University Medical Center
Department Biochemistry
Lab 652 PRB
Street address 23rd Ave South at Pierce
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platform ID GPL570
Series (1)
GSE4975 Expression data from p63 siRNA in squamous cell lines

Data table header descriptions
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
AFFX-BioB-5_at 429 P
AFFX-BioB-M_at 441.1 P
AFFX-BioB-3_at 201.7 P
AFFX-BioC-5_at 750.2 P
AFFX-BioC-3_at 635.6 P
AFFX-BioDn-5_at 1141.8 P
AFFX-BioDn-3_at 4494.5 P
AFFX-CreX-5_at 9426.7 P
AFFX-CreX-3_at 12714.6 P
AFFX-DapX-5_at 52.6 A
AFFX-DapX-M_at 137.2 A
AFFX-DapX-3_at 13.2 A
AFFX-LysX-5_at 58.3 A
AFFX-LysX-M_at 124.7 A
AFFX-LysX-3_at 45.3 A
AFFX-PheX-5_at 11.9 A
AFFX-PheX-M_at 7.8 A
AFFX-PheX-3_at 35.6 A
AFFX-ThrX-5_at 12.5 A
AFFX-ThrX-M_at 31.7 A

Total number of rows: 54675

Table truncated, full table size 983 Kbytes.

Supplementary data files not provided

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