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Sample GSM570071 Query DataSets for GSM570071
Status Public on Jul 21, 2011
Title TNF treated collagen culture, biological rep3
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)
 
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.

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
10701620 3.273236
10701630 2.283672
10701632 2.473415
10701636 1.985318
10701643 2.110674
10701648 2.793819
10701654 2.871642
10701663 6.509235
10701666 2.188206
10701668 3.113488
10701671 2.321848
10701674 2.504164
10701679 3.743832
10701684 4.810729
10701689 3.449236
10701691 4.634117
10701697 5.440778
10701699 7.011364
10701709 9.607791
10701714 4.591942

Total number of rows: 27342

Table truncated, full table size 477 Kbytes.




Supplementary file Size Download File type/resource
GSM570071_Col_TNF_GL16.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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