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Sample GSM455804 Query DataSets for GSM455804
Status Public on Sep 24, 2009
Title Dosed with CDC6 tobacco product, biological rep1
Sample type RNA
 
Source name Dosed with CDC6 tobacco product
Organism Homo sapiens
Characteristics cell type: Primary human bronchial/tracheal epithelial cells
Treatment protocol NHBE cells were treated for 18 hr with cigarette smoke condensates (CSCs) prepared from 5 commercial and 4 research cigarettes, at doses of ~ 4 μg/ml nicotine.
Growth protocol Primary human bronchial/tracheal epithelial (NHBE) cells were grown in tissue culture.
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy used for total RNA extraction and was performed according to manufacture's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Affymetrix One-Cycle Target Labeling Kit).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133 2.0+ Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description CDC6_1
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 500.
 
Submission date Sep 23, 2009
Last update date Sep 23, 2009
Contact name Gavin Pickett
Organization name UNM
Department Genomics
Lab KUGR
Street address 2325 Camino de Salud NE
City Albuquerque
State/province NM
ZIP/Postal code 87131
Country USA
 
Platform ID GPL570
Series (1)
GSE18235 Effect of 10 Cigarette Smoke Condensates on Primary Human Airway Epithelial Cells

Data table header descriptions
ID_REF
VALUE MAS 5.0 Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 168.013 P 0.000195116
AFFX-BioB-M_at 267.37 P 4.42873e-05
AFFX-BioB-3_at 160.158 P 4.42873e-05
AFFX-BioC-5_at 456.189 P 4.42873e-05
AFFX-BioC-3_at 516.783 P 4.42873e-05
AFFX-BioDn-5_at 1080.88 P 4.42873e-05
AFFX-BioDn-3_at 1983.59 P 4.42873e-05
AFFX-CreX-5_at 5159.66 P 4.42873e-05
AFFX-CreX-3_at 6582.78 P 4.42873e-05
AFFX-DapX-5_at 577.122 P 4.42873e-05
AFFX-DapX-M_at 796.086 P 7.00668e-05
AFFX-DapX-3_at 1168.16 P 4.42873e-05
AFFX-LysX-5_at 58.2578 P 0.000169227
AFFX-LysX-M_at 88.2032 P 0.00012664
AFFX-LysX-3_at 148.091 P 4.42873e-05
AFFX-PheX-5_at 113.558 P 5.16732e-05
AFFX-PheX-M_at 157.962 P 6.02111e-05
AFFX-PheX-3_at 136.901 P 4.42873e-05
AFFX-ThrX-5_at 163.444 P 4.42873e-05
AFFX-ThrX-M_at 202.174 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1642 Kbytes.




Supplementary file Size Download File type/resource
GSM455804.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM455804.CHP.gz 302.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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