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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2008 |
| Title |
Genomic profile of IL10-/- knocked out colitis model |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Objetives: study and characterization of the IL10-/- knocked out colitis model in mice at genomic level and the study of the influence of bacteria in the development of the disease.
Keywords: Differentially expressed genes analysis
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| Overall design |
We used three groups of animasl: 1)IL10-/- mice grown under conventional condition, 2)IL10-/- mice grown under specific pathogen free (SPF) conditions, 3) Wild type mice grown under conventional conditions (CONTROL group). For each group, we recovered samples at 7, 9 and 12 weeks after birth According to colon length and colonic damage, three replicates were selected for each time point and each group (27 samples), for genomic analysis.
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, Gil A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Oct 11, 2007 |
| Last update date |
Feb 11, 2019 |
| 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) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
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| Samples (27)
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| GSM236929 |
7SPF, replicate 1 |
| GSM236930 |
7SPF, replicate 2 |
| GSM236931 |
7SPF, replicate 3 |
| GSM236932 |
7WT, replicate 1 |
| GSM236933 |
7WT, replicate 2 |
| GSM236934 |
7WT, replicate 3 |
| GSM236940 |
9CC, replicate 1 |
| GSM236959 |
9CC, replicate 2 |
| GSM236960 |
9CC, replicate 3 |
| GSM236961 |
9SPF, replicate 1 |
| GSM236963 |
9SPF, replicate 2 |
| GSM236965 |
9SPF, replicate 3 |
| GSM236967 |
9WT, replicate 1 |
| GSM236968 |
9WT, replicate 2 |
| GSM236969 |
9WT, replicate 3 |
| GSM236970 |
12CC, replicate 1 |
| GSM236971 |
12CC, replicate 2 |
| GSM236972 |
12CC, replicate 3 |
| GSM236973 |
12SPF, replicate 1 |
| GSM236974 |
12SPF, replicate 2 |
| GSM236975 |
12SPF, replicate 3 |
| GSM236976 |
12WT, replicate 1 |
| GSM236977 |
12WT, replicate 2 |
| GSM236978 |
12WT, replicate 3 |
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| Relations |
| BioProject |
PRJNA102941 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9297_RAW.tar |
92.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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