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Sample GSM460113 Query DataSets for GSM460113
Status Public on Jul 13, 2010
Title FOX_HIF_HYPOXIA_rep1
Sample type RNA
 
Source name FOX_HIF_HYPOXIA
Organism Mus musculus
Characteristics tissue: prostate tumor
strain: C57BL6
sex: male
cell type: TRAMP-C
Treatment protocol TRAMP-C cells were transfected with pcDNA, or FoxA2, or HIF-1a, or HIF-1a + FoxA2 using Amax Nucleofector in duplicate. 48 hour post transfection, cells were treated with normoxia or 1% hypoxia for 12 h before isolation of total RNA. 500 ng of total RNA was used for synthesis of biotin-labeled cRNA using an RNA amplification kit (Ambion). The biotinylated cRNA is labeled by incubation with streptavidin-Cy3 to generate probe for hybridization with the Mouse-6 Expression BeadChip (Illumina) that represents 48K mouse gene transcripts.
Growth protocol TRAMP-C cells were isotated from the prostate tumor of TRAMP mice, which is C57BL6. The TRAMP-C cells are wild-type.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label streptavidin Cy3
Label protocol As suggested by illumina
 
Hybridization protocol As recommended by illumina
Scan protocol As suggested by illumina using the illumina scanner
Description 4323501009_B
Data processing Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine
 
Submission date Oct 08, 2009
Last update date Jul 02, 2010
Contact name Roy M Williams
E-mail(s) rwillia@scripps.edu
Organization name The Scripps Research Institute
Department Regenerative Medicine
Lab Loring
Street address 3030 Science Park Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL6887
Series (1)
GSE18478 Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine prostate tumors

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2545897 49.09166667 0.04915
ILMN_2707227 188.5833333 0
ILMN_2896528 1682.566667 0
ILMN_2721178 252.4833333 0
ILMN_1227723 231.3083333 0
ILMN_3033922 290.775 0
ILMN_3092673 1628.908333 0
ILMN_1230777 1086.941667 0
ILMN_2730714 2372.05 0
ILMN_1246069 351.1916667 0
ILMN_1243193 967.5 0
ILMN_2524361 50.575 0.03205
ILMN_1233188 425.225 0
ILMN_2543688 493.5458333 0
ILMN_3162224 918.8291667 0
ILMN_2816356 65.35 0.00107
ILMN_1224596 154.7708333 0
ILMN_1233643 108.1041667 0
ILMN_2808939 886.7583333 0
ILMN_2771349 109.4125 0

Total number of rows: 26415

Table truncated, full table size 723 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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