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Sample GSM112329 Query DataSets for GSM112329
Status Public on Jun 06, 2006
Title SCC-6 cells transfected with control vector
Sample type RNA
Source name SCC-6 cells transfected with control vector
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 control vector
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 419.4 P
AFFX-BioB-M_at 478.3 P
AFFX-BioB-3_at 227.9 P
AFFX-BioC-5_at 812.3 P
AFFX-BioC-3_at 813.4 P
AFFX-BioDn-5_at 1168.7 P
AFFX-BioDn-3_at 3869.6 P
AFFX-CreX-5_at 9931 P
AFFX-CreX-3_at 12234.9 P
AFFX-DapX-5_at 86.9 A
AFFX-DapX-M_at 78.2 A
AFFX-DapX-3_at 64.1 A
AFFX-LysX-5_at 56 A
AFFX-LysX-M_at 22.4 A
AFFX-LysX-3_at 24.2 A
AFFX-PheX-5_at 5.5 A
AFFX-PheX-M_at 14.1 A
AFFX-PheX-3_at 18.8 A
AFFX-ThrX-5_at 14.6 A
AFFX-ThrX-M_at 22.2 A

Total number of rows: 54675

Table truncated, full table size 981 Kbytes.

Supplementary data files not provided

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