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Sample GSM417883 Query DataSets for GSM417883
Status Public on Jun 24, 2009
Title TCDD 3
Sample type RNA
Source name 100 nM TCDD
Organism Xenopus laevis
Characteristics cell line: XLK-WG
Treatment protocol Cells were treated with dimethylsulfoxide (DMSO) vehicle (0.25%) or 100 nM TCDD or 100 nM FICZ dissolved in DMSO (vehicle concentration also 0.25%)
Growth protocol Cells were grown to 90% confluence in 25 cm2 flasks
Extracted molecule total RNA
Extraction protocol RNA was extracted using QIAshedder spin columns and RNeasy kits (Qiagen, Hilden, Germany) per the procedure supplied by the manufacturer.
Label biotin
Label protocol Probes were labeled by the University of Wisconsin Biotechnology CenterÕs Gene Expression Microarray Facility in Madison, Wisconsin using the MessageAmp II-Biotin Enhanced kit (Ambion). Input is 1 ug RNA.
Hybridization protocol Samples were hybridized to Xenopus laevis GeneChips (Affymetrix, Santa Clara, CA) according to manufacturer's protocol.
Scan protocol Hybridized chips were scanned using Affymetrix GC3000 7G scanning equipment.
Description TCDD 3 (biological rep)
Data processing Affymetrix GCOS software. Gene expression was determined using the PM/MM method in dChip (Build: Sept 10, 2007). Statistical analysis was completed via 2-way ANOVA with individual contrasts (p£0.01) using Statistical Analysis Software (SAS; Cary, NC)
Submission date Jun 17, 2009
Last update date Jun 24, 2009
Contact name Wade H Powell
Phone 740-427-5396
Fax 740-427-5741
Organization name Kenyon College
Department Biology Dept.
Street address 302A College Park St.
City Gambier
State/province OH
ZIP/Postal code 43022
Country USA
Platform ID GPL1318
Series (1)
GSE16670 Responsiveness of a frog cell line to the AHR ligands FICZ and TCDD

Data table header descriptions
VALUE log2 dChip signal

Data table
AFFX-BioB-5_at 7.998
AFFX-BioB-M_at 7.972
AFFX-BioB-3_at 7.742
AFFX-BioC-5_at 8.805
AFFX-BioC-3_at 9.387
AFFX-BioDn-5_at 9.836
AFFX-BioDn-3_at 11.031
AFFX-CreX-5_at 12.629
AFFX-CreX-3_at 12.921
AFFX-DapX-5_at 8.563
AFFX-DapX-M_at 9.156
AFFX-DapX-3_at 9.334
AFFX-LysX-5_at 5.597
AFFX-LysX-M_at 6.902
AFFX-LysX-3_at 6.962
AFFX-PheX-5_at 6.056
AFFX-PheX-M_at 7.023
AFFX-PheX-3_at 6.77
AFFX-ThrX-5_at 5.825
AFFX-ThrX-M_at 6.857

Total number of rows: 15611

Table truncated, full table size 345 Kbytes.

Supplementary file Size Download File type/resource
GSM417883.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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