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Sample GSM159485 Query DataSets for GSM159485
Status Public on Jun 21, 2007
Title Sham infected HIGK cells, biological rep1
Sample type RNA
 
Source name Gene expression data from sham infected HIGK cells.
Organism Homo sapiens
Characteristics HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
Treatment protocol HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.
Growth protocol HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
Label biotin
Label protocol cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
 
Hybridization protocol Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
Scan protocol GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
Description Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
Data processing The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Jan 31, 2007
Last update date Jun 21, 2007
Contact name Martin Handfield
E-mail(s) mhandfield@dental.ufl.edu
Phone 352-846-0763
Organization name University of Florida
Department Oral Biology
Lab Handfield Lab
Street address 1600 SW Archer Road, BOX 100424
City Gainesville
State/province FL
ZIP/Postal code 32610-0424
Country USA
 
Platform ID GPL96
Series (1)
GSE6927 Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial Species.

Data table header descriptions
ID_REF 2490
VALUE GCOS-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)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 780.6 P 0.000972
AFFX-BioB-M_at 1240 P 0.000052
AFFX-BioB-3_at 850.2 P 0.000195
AFFX-BioC-5_at 1613.8 P 0.00011
AFFX-BioC-3_at 1407.6 P 0.00007
AFFX-BioDn-5_at 1623.2 P 0.000081
AFFX-BioDn-3_at 9894.6 P 0.000195
AFFX-CreX-5_at 16690.6 P 0.000044
AFFX-CreX-3_at 26419.7 P 0.000044
AFFX-DapX-5_at 46.9 A 0.275146
AFFX-DapX-M_at 29.5 A 0.327079
AFFX-DapX-3_at 5.6 A 0.957038
AFFX-LysX-5_at 9.4 A 0.58862
AFFX-LysX-M_at 16 A 0.794268
AFFX-LysX-3_at 9.9 A 0.5
AFFX-PheX-5_at 7.4 A 0.737173
AFFX-PheX-M_at 13.6 A 0.814869
AFFX-PheX-3_at 30.8 A 0.686277
AFFX-ThrX-5_at 19.6 A 0.783476
AFFX-ThrX-M_at 30 A 0.51489

Total number of rows: 22283

Table truncated, full table size 594 Kbytes.




Supplementary file Size Download File type/resource
GSM159485.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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