|
| Status |
Public on Mar 12, 2014 |
| Title |
IL-10-deficient_Infected |
| Sample type |
RNA |
| |
|
| Source name |
IL-10-deficient_Infected_whole colon
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: IL-10-/-; IL-10 deficient
gender: female
age: 10 weeks
infected with: 200 µl of C. rodentium DBS100 (5 x 10^8 CFU/mouse)
tissue: whole colon
|
| Treatment protocol |
8-wk-old mice were infected by oral gavage with 200 µl of Citrobacter rodentium strain DBS100 (5 x 10^8 CFU/mouse).
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (isolated with TRIzol reagent) was prepared from whole colonic tissue of WT and IL-10-/- mice before or 2 weeks after infection with Citrobacter rodentium.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Quick Amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
1650ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). 5 µm scanning in green at 10% and 100% PMT
|
| Description |
Gene expression in whole colonic tissue from infected IL-10-deficient mice
|
| Data processing |
the protocol used for extraction was GE1_107_Sep09. Version 10.7.3.1. of feature extraction. The data were normalized using the multi-loess method described in this paper: Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil, J. Mol. Endocrinology, 33, 1 (2004)
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| |
|
| Submission date |
Mar 11, 2014 |
| Last update date |
Mar 12, 2014 |
| Contact name |
Lars Eckmann |
| E-mail(s) |
[email protected]
|
| Organization name |
University of San Diego
|
| Department |
Gastroenterology
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0063 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE55812 |
Gene expression in IL-10-deficient and wild-type mice following Citrobacter rodentium infection |
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