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| Status |
Public on Nov 01, 2008 |
| Title |
Genomic profile of dextran sulphate sodium-induced colitis model in rats |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
Background & Aims: Dextran sulphate sodium (DSS) induced colitis in rats is one of the most widely used models of inflammatory bowel disease. Animal models can provide new insights into the pathogenesis of intestinal inflammation, which is still unknown. We have performed a genomic analysis of the DSS rat colitis including an acute and a recovery phase. Methods: Expression profile of 6 control rats were compared with colitic rats at day 1 every other day until day 23 after DSS treatment using the GeneChip Rat Genome 230 2.0 Array (Affymetrix). Functional and pathways analysis were made with the differentially expressed genes.
Keywords: Time course and differentially expressed genes analysis
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| Overall design |
Experimental design: DSS was administered to animals in drinking water as follows:5%DSS from day 1 to 7, 3%DSS from day 8 to 15, 0% DSS from day 16 to 23. Samples were recovered at days 1, 3, 5, 7 (5%DSS), 9, 11, 13, 15 (2%DSS), 17, 19, 21 and 23 (0%DSS). According to inflammatory markers (Myeloperoxidase activity activity, body weight loss, colonic weigth/length ratio), three replicates at each time point were selected for genomic analysis and 6 control healthy rats (42 arrays).
RNA was extracted from homogenized full-thickness colonic tissues in Trizol® reagent (Invitrogen) and purified with RNeasy affinity columns (Qiagen), according to manufacturer´s protocol. The microarray analysis was performed by Progenika Biopharma (Bilbao, Spain) on GeneChip® Rat Genome 230 2.0 Array (Affymetrix). All sample labeling (biotin), hybridization, staining and scanning procedures were carried out using Affimetrix, standard protocols (www.affymetrix.com). Normalization was carried out using Bioconductor sofware (affyPLM package).
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| Contributor(s) |
Montero T, Suárez A, Llor X, Gassull MA, Sánchez de Medina F, Martínez O, Vieites JM, Gil A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 10, 2007 |
| Last update date |
Jul 31, 2017 |
| Contact name |
Antonio Suarez |
| E-mail(s) |
asuarez@ugr.es
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| Phone |
+34 958242335
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| Organization name |
University of Granada
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| Department |
Biochemistry and Molecular Biology
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| Street address |
Pharmacy Faculty, Campus Cartuja s/n
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| City |
Granada |
| State/province |
Granada |
| ZIP/Postal code |
18071 |
| Country |
Spain |
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| Platforms (1) |
| GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
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| Samples (42)
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| GSM235056 |
Healthy control, replicate 4 |
| GSM235057 |
Healthy control, replicate 5 |
| GSM235058 |
Healthy control, replicate 6 |
| GSM235059 |
DSS day1, replicate 1 |
| GSM235060 |
DSS day 1, replicate 2 |
| GSM235061 |
DSS day 1, replicate 3 |
| GSM235062 |
DSS day 3, replicate 1 |
| GSM235063 |
DSS day 3, replicate 2 |
| GSM235064 |
DSS day 3, replicate 3 |
| GSM235066 |
DSS day 5, replicate 1 |
| GSM235067 |
DSS day 5, replicate 2 |
| GSM235068 |
DSS day 5, replicate 3 |
| GSM235069 |
DSS day 7, replicate 1 |
| GSM235070 |
DSS day 7, replicate 2 |
| GSM235072 |
DSS day 7, replicate 3 |
| GSM235508 |
DSS day 9, replicate 1 |
| GSM235509 |
DSS day 9, replicate 2 |
| GSM235510 |
DSS day 9; replicate 3 |
| GSM235511 |
DSS day 11, replicate 1 |
| GSM235512 |
DSS day 11, replicate 2 |
| GSM235513 |
DSS day 11, replicate 3 |
| GSM235514 |
DSS day 13, replicate 1 |
| GSM235515 |
DSS day 13, replicate 2 |
| GSM235516 |
DSS day 13, replicate 3 |
| GSM235517 |
DSS day 15, replicate 1 |
| GSM235518 |
DSS day 15, replicate 2 |
| GSM235519 |
DSS day 15, replicate 3 |
| GSM235520 |
DSS day 17, replicate 1 |
| GSM235521 |
DSS day 17, replicate 2 |
| GSM235522 |
DSS day 17, replicate 3 |
| GSM235523 |
DSS day 19, replicate 1 |
| GSM235524 |
DSS day 19, replicate 2 |
| GSM235525 |
DSS day 19, replicate 3 |
| GSM235526 |
DSS day 21, replicate 1 |
| GSM235527 |
DSS day 21, replicate 2 |
| GSM235528 |
DSS day 21, replicate 3 |
| GSM235529 |
DSS day 23, replicate 1 |
| GSM235530 |
DSS day 23, replicate 2 |
| GSM235531 |
DSS day 23, replicate 3 |
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| Relations |
| BioProject |
PRJNA102915 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9281_RAW.tar |
95.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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