|
| Status |
Public on Oct 15, 2013 |
| Title |
Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection mRNA rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Extrahepatic Bileduct and gallbladder en bloc at day 3 after normal saline injection
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Extrahepatic Bileduct and gallbladder
strain: Balb/c
time: 3 days
treatment: Normal saline injection
|
| 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 bile ducts.
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 |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).
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| |
|
| Hybridization protocol |
Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45 ˚C on the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
The data were analyzed with GeneSpring GX 11.5 using RMA normalization, then normalized to the median of all samples
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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 |
GPL6246 |
| Series (2) |
| GSE41594 |
Comprehensive gene expression profile of mouse extrahepatic bileducts and gallbladder during a mouse model of biliary atresia. |
| GSE41595 |
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia |
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