|
| Status |
Public on Oct 15, 2013 |
| Title |
Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge miRNA rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Extrahepatic Bileduct and gallbladder en bloc at day 3 after rhusus rotvirus challenge
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Extrahepatic Bileduct and gallbladder
strain: Balb/c
time: 3 days
treatment: Rhesus rotavirus
|
| Treatment protocol |
Newborn mice were injected with 20 μL of a solution containing 1.5x10^6 fluorescent-forming units of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth.
|
| Growth protocol |
Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extrahepatic bile ducts and gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injection and stabilized with RNAlater (QIAGEN, CA).
3 sets of samples were generated for each time point (experimental and control groups), with each set containing 2-6 extrahepatic bileducts.
Total RNA was isolated from extrahepatic bileducts of RRV- or saline-injected mice using miRNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).
|
| Label |
FAM
|
| Label protocol |
Reverse transcription into first strand cDNA was performed using reagents from TaqMan® MicroRNA RT Kit and Megaplex RT Primer Pools (Applied Biosystems, CA).
Quantitative real-time PCR was performed using the TaqMan® Array Rodent MicroRNA Card v2.0 (A and B) with the Universal PCR Master Mix, No AmpErase UNG using 7900 HT Fast Real-Time PCR System (Applied Biosystems).
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| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Experimental group at day 3
|
| Data processing |
Expression was calculated using the comparative Ct method (Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3: 1101-8)
Normalization was done using average of 4 MammU6 probes on each plate.
The deltaCt values (Ct_Target − Ct_MammU6) were imported to GeneSpring GX 11.5 platform (Agilent Technologies, CA), converted to log2-based values and used for statistical analyses.
Fold Change worksheet reports each sample/average of 9 normal controls (i.e., D3_NS_1~3, D7_NS_1~3, D14_NS_1~3) ratios.
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| |
|
| Submission date |
Oct 15, 2012 |
| Last update date |
Oct 15, 2013 |
| Contact name |
Jorge A Bezerra |
| E-mail(s) |
jorge.bezerra@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Gastroenterology, Hepatology & Nutrition
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL15053 |
| Series (2) |
| GSE41593 |
Taqman Low Density Arrays (TLDA) based microRNAs expression profile of mouse extrahepatic bileducts and gallbladders during a mouse model of biliary atresia. |
| GSE41595 |
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia |
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