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Sample GSM112325 Query DataSets for GSM112325
Status Public on Jun 06, 2006
Title HaCaT cells transfected with control vector
Sample type RNA
Source name HaCaT cells transfected with control vector
Organism Homo sapiens
Characteristics immortalized keratinocyte cells

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 HaCaT 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 468.7 P
AFFX-BioB-M_at 497 P
AFFX-BioB-3_at 298.1 P
AFFX-BioC-5_at 877.4 P
AFFX-BioC-3_at 710.7 P
AFFX-BioDn-5_at 1339.1 P
AFFX-BioDn-3_at 4110 P
AFFX-CreX-5_at 9741.2 P
AFFX-CreX-3_at 12543.6 P
AFFX-DapX-5_at 29.1 A
AFFX-DapX-M_at 42.6 A
AFFX-DapX-3_at 32.8 A
AFFX-LysX-5_at 34.9 A
AFFX-LysX-M_at 20.7 A
AFFX-LysX-3_at 7.7 A
AFFX-PheX-5_at 3.3 A
AFFX-PheX-M_at 8.2 A
AFFX-PheX-3_at 8.3 A
AFFX-ThrX-5_at 17.1 A
AFFX-ThrX-M_at 57.7 A

Total number of rows: 54675

Table truncated, full table size 978 Kbytes.

Supplementary data files not provided

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