|
| Status |
Public on Jul 23, 2014 |
| Title |
colon_DSS_c45_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
colon_DSS_c45_rep2
|
| Organism |
Mus musculus |
| Characteristics |
strain: c57BL/6
tissue: colon
genotype: wild type
group: DSS-c4d5
|
| Treatment protocol |
Wild type c57BL/6 mice were fed ad libitum with 2.5% (wt/vol) dextran sodium sulfate (DSS, 40KDa, ICN Biochemicals, Aurora, OH) in drinking water for 1, 3 or 5 days to induce acute phase colitis. To induce chronic colitis, C57BL/6 mice were supplied with 2.5% DSS in drinking water for 5 days and switched back to normal drinking water for 9 days before the next cycles. Four cycles of the DSS treatment were used in the study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Hy3
|
| Label protocol |
not provided
|
| |
|
| Channel 2 |
| Source name |
Total RNA from pooled from individual samples
|
| Organism |
Mus musculus |
| Characteristics |
group: reference
|
| Treatment protocol |
Wild type c57BL/6 mice were fed ad libitum with 2.5% (wt/vol) dextran sodium sulfate (DSS, 40KDa, ICN Biochemicals, Aurora, OH) in drinking water for 1, 3 or 5 days to induce acute phase colitis. To induce chronic colitis, C57BL/6 mice were supplied with 2.5% DSS in drinking water for 5 days and switched back to normal drinking water for 9 days before the next cycles. Four cycles of the DSS treatment were used in the study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Hy5
|
| Label protocol |
not provided
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)
|
| Description |
Hy3: Mice were sacrificed 5 days after 4 cycles of DSS treatment
DSS-c4d5_2
|
| Data processing |
image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Annotation is based on miRBASE version 14.0
|
| |
|
| Submission date |
Jul 22, 2014 |
| Last update date |
Jul 23, 2014 |
| Contact name |
Yong Huang |
| E-mail(s) |
yh9fj@virginia.edu
|
| Phone |
(434) 243-0842
|
| Organization name |
University of Viginia
|
| Department |
Medicine
|
| Street address |
1340 Jefferson Park Ave
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL7723 |
| Series (2) |
| GSE59649 |
Divergent influence of microRNA-21 deletion on murine colitis phenotypes [DSS] |
| GSE59651 |
Divergent influence of microRNA-21 deletion on murine colitis phenotypes |
|
