|
| Status |
Public on Jul 23, 2014 |
| Title |
colon_control_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
colon_control_rep1
|
| Organism |
Mus musculus |
| Characteristics |
strain: c57BL/6
tissue: colon (cross section)
genotype: wild type
group: Control
|
| Treatment protocol |
Wild type c57BL/6 mice were sensitized by application of 1% 2-4-6-trinitrobenzenesulphonic acid (TNBS) (Sigma Chemical Co., St. Louis, MO) in 50% ethanol on skin on day -7 (week 1). On day 0 (week 2), mice were given an enema of 5ul/g body weight of 2.5% TNBS in 50% ethanol under anesthesia. Subsequent TNBS enema was repeated on day 7 (week 3) and 14 (week 4). Mice were sacrificed 2 days after the second cycle (w2d2) for the assessment of acute colitis and 2 days after the fourth cycle (w4d2) for the assessment of chronic colitis. A group of mice were sacrificed 7 days after the fourth cycle (w4d7 or w5d2), representing recovering phase of colitis.
|
| 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 sensitized by application of 1% 2-4-6-trinitrobenzenesulphonic acid (TNBS) (Sigma Chemical Co., St. Louis, MO) in 50% ethanol on skin on day -7 (week 1). On day 0 (week 2), mice were given an enema of 5ul/g body weight of 2.5% TNBS in 50% ethanol under anesthesia. Subsequent TNBS enema was repeated on day 7 (week 3) and 14 (week 4). Mice were sacrificed 2 days after the second cycle (w2d2) for the assessment of acute colitis and 2 days after the fourth cycle (w4d2) for the assessment of chronic colitis. A group of mice were sacrificed 7 days after the fourth cycle (w4d7 or w5d2), representing recovering phase of colitis.
|
| 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: Control mouse received H2O enema
|
| 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) |
[email protected]
|
| 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) |
| GSE59650 |
Divergent influence of microRNA-21 deletion on murine colitis phenotypes [TNBS] |
| GSE59651 |
Divergent influence of microRNA-21 deletion on murine colitis phenotypes |
|
