|
| Status |
Public on Jan 24, 2012 |
| Title |
Pdx1-Cre;KrasLSL-G12D vs. Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F pancreatic tissues |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cDNA from Pdx1-Cre;KrasLSL-G12D pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 and 129
genotype: Pdx1-Cre;KrasLSL-G12D
tissue: pancreatic tumor
|
| Biomaterial provider |
Jianhua Ling
|
| Treatment protocol |
None.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mouse pancreata using the Trizol method. The integrity and purity of RNA was determined by the Agilent BioAnalyzer.
|
| Label |
Cy3
|
| Label protocol |
Performed by following the protocol provided by Agilent.
|
| |
|
| Channel 2 |
| Source name |
cDNA from Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 and 129
genotype: Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F
tissue: normal pancreas
|
| Biomaterial provider |
Jianhua Ling
|
| Treatment protocol |
None.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mouse pancreata using the Trizol method. The integrity and purity of RNA was determined by the Agilent BioAnalyzer.
|
| Label |
Cy5
|
| Label protocol |
The Core Lab performed probe labeling using the protocol provided by Agilent.
|
| |
|
| |
| Hybridization protocol |
The Core Lab performed the hybridization using the protocol provided by Agilent. Microarray experiments were carried out using whole human genome oligo arrays with 44k 60-mer probes (Agilent Technologies, Palo Alto, CA) with 500 ng of total RNA starting material.
|
| Scan protocol |
The Core Lab performed image acquisition using the protocol provided by Agilent. The hybridized arrays were scanned with Agilent's dual laser-based scanner.
|
| Data processing |
Feature Extraction software version 8.0 (Agilent Technologies) was used to link a feature to a design file and to determine the relative fluorescence intensity between the two samples. The VALUEs in the Sample data table represent Lowess-normalized log10 ratios (Cy5/Cy3). The VALUES in the 'GSE27478_fold_change_data.txt' file (which is linked to the Series GSE27478 record as a supplementary file) are the fold changes of KrasD/+,PDX1-CRE:KrasD/+, PDX1-CRE,IKK2F/ MICE. The detailed statistical analysis was performed as described by Price et al. Proc Natl Acad Sci USA. 2007 Feb 27;104(9):3414-9 (PMID 17360660).
|
| |
|
| Submission date |
Feb 23, 2011 |
| Last update date |
Jan 24, 2012 |
| Contact name |
Paul J Chiao |
| E-mail(s) |
[email protected]
|
| Phone |
(713) 794-1030
|
| Fax |
(713) 794-4830
|
| Organization name |
The University of Texas M. D. Anderson Cancer Center
|
| Department |
Department of Molecular and Cellular Oncology
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
770300 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE27478 |
Gene expression differences between the pancreatic tissues of Pdx1-Cre;KrasLSL-G12D and Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F mice |
| GSE33323 |
Kras-induced ikk2/nf-kappaB activation by IL-1 alpha and p62 freedforward loops is required for development of pancreatic ductal adenocarcinoma |
|
