|
| Status |
Public on Mar 12, 2015 |
| Title |
RF-229 primary |
| Sample type |
RNA |
| |
|
| Source name |
primary OS that produced metastatic lesion_RF-229 specimen
|
| Organism |
Mus musculus |
| Characteristics |
sample group: primary OS that produced metastatic lesion
specimen id: RF-229 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.
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| |
|
| 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 |
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