|
| Status |
Public on Jul 21, 2011 |
| Title |
TNF treated collagen culture, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
TNF treated collagen gel culture of aortic ring, day 2
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: TNF treated collagen
tissue: aortic rings cultured in collagen gels
genotype: Fisher 344
gender: male
age: 1-2 month old rat aortas
|
| Treatment protocol |
Collagen or fibrin gels containing aortic rings were washed in PBS, transferred to buffer RLT from the Qiagen RNAEasy kit, and snap frozen in liquid nitrogen.
|
| Growth protocol |
Four to six individual aortic ring cultures from each treatment groupd were combined to generate a sample. All cultures were grown in serum free EBM medium (Lonza). Samples were divided into treatment groups receiving 10ng/ml recombinant Rat TNFa or left untreated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following pulverization under liquid nitrogen, extraction of total RNA was performed with a microRNA Easy kit from Qiagen according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to standard Affymetrix Whole Transcript Sense Labeling Protocol from 200 ng of total RNA. (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay User Manual, P/N 701880 Rev. 5)
|
| |
|
| Hybridization protocol |
Following fragmentation, 10ug of cRNA was hybridized for 17 hr at 45 degrees C on Affymetrix Rat Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Gene Chip Fluidics Station 450.)
|
| Scan protocol |
Affymetrix Rat Gene 1.0 ST Arrays were scanned using the Affymetrix GeneChip® 3000 scanner.
|
| Description |
Gene expression in TNF treated collagen gel cultures or rat aorta at day 2
|
| Data processing |
Raw microarray data were processed with Bioconductor (http://www.bioconductor.org/) Probes were normalized with the Robust Multi-Array normalization procedure (Irizarry RA, Gautier L, Cope L, eds. An r package for analyses of affymetrix oligonucleotide arrays. London: Springer; 2003. Parmigiani RIG, Garrett ES, Zeger S, eds. The analysis of gene expression data: Methods and software.) From the normalized data, genes with significant evidence for differential expression were identified using the Bioconductor limma package (Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology. 2004;3:3)
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| |
|
| Submission date |
Jul 26, 2010 |
| Last update date |
Jul 21, 2011 |
| Contact name |
Alfred C Aplin |
| E-mail(s) |
aaplin@u.washington.edu
|
| Phone |
206-277-1528
|
| Organization name |
University of Washington
|
| Department |
Pathology
|
| Street address |
Box 357470 HSB-UW
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE23153 |
Gene expression in TNF treated rat aortic rings cultured in collagen or fibrin gels. |
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