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Sample GSM1059943 Query DataSets for GSM1059943
Status Public on Mar 12, 2015
Title RF-104 primary
Sample type RNA
 
Source name primary OS that produced metastatic lesion_RF-104 specimen
Organism Mus musculus
Characteristics sample group: primary OS that produced metastatic lesion
specimen id: RF-104 specimen
Growth protocol Three genetically engineered mouse lines were used in this study. Col2.3-Cre mice contain a rat Col1a1 2.3 kb rat promoter driving a Cre transgene (Liu et al., 2004) These mice express Cre in osteoblast lineages. These mice were backcrossed into a C57BL/6 background and further crossed to either floxed p53 mice or LSL-p53R172H mice. Floxed p53 mice were generated by the Berns laboratory (Marino et al., 2000) and obtained from the NCI Mouse Repository. These mice were also backcrossed into a C57BL/6 background and contain a wildtype p53 allele that can be excised by Cre recombinase binding to LoxP sites located in introns 1 and 10 of the p53 gene. The LSL-p53R172H mice were made by the Jacks laboratory (Olive et al., 2004), obtained from the NCI Mouse Repository and backcrossed into a C57BL/6 background. These mice contain a “hot spot” point-mutant allele of Trp53 frequently observed in human tumors that can be activated by Cre-mediated deletion of the lox-stop-lox (LSL) cassette located in the altered p53 promoter. All mice were bred and maintained in a specific pathogen-free animal facility at Baylor College of Medicine. All research with mice was conducted in compliance with the Baylor Animal Protocol Committee (Baylor College of Medicine Animal Protocol AN336) and AAALAC recommendations as published in The Guide for the Care and Use of Laboratory Animals (NRC1996).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissue samples, using Trizol. RNA quality were inspected on a 2100 Bioanalyzer (Agilent).
Label biotin
Label protocol According to Illumina protocol.
 
Hybridization protocol According to Illumina protocol.
Scan protocol According to Illumina protocol.
Data processing The image data were compiled into a project using Beadstudio software gene expression module version 3.2.7. No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format (please note that the ID_REF column in raw data files contains 'Array_Address_Id'). The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.
 
Submission date Jan 04, 2013
Last update date Mar 12, 2015
Contact name Chad Creighton
E-mail(s) creighto@bcm.tmc.edu
Organization name Baylor College of Medicine
Department Biostatistics, Ducan Cancer Center
Street address One Baylor Plaza, Mail Stop: BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6887
Series (1)
GSE43281 Gene expression analyses of primary tumors and metastases, using p53 mouse models

Data table header descriptions
ID_REF
VALUE 'signal' a measure of the abundance of a transcript

Data table
ID_REF VALUE
ILMN_2735294 5.832383717
ILMN_2417611 5.413627929
ILMN_2545897 6.640458974
ILMN_2762289 5.586464526
ILMN_1248788 5.311067102
ILMN_2707227 5.768562817
ILMN_2896528 11.18878064
ILMN_2721178 8.61868906
ILMN_1227723 9.299852736
ILMN_2458837 5.241702923
ILMN_3033922 9.996636886
ILMN_3092673 12.18358393
ILMN_1230777 11.71069913
ILMN_2730714 12.34893981
ILMN_1246069 11.00737115
ILMN_1232042 5.389738879
ILMN_1243193 10.27544478
ILMN_2524361 5.590961241
ILMN_1233188 7.709497429
ILMN_2543688 10.76821675

Total number of rows: 45281

Table truncated, full table size 1100 Kbytes.




Supplementary file Size Download File type/resource
GSM1059943_RF-104_primary.txt.gz 664.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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