|
| Status |
Public on Sep 07, 2023 |
| Title |
BVC5018 |
| Sample type |
RNA |
| |
|
| Source name |
Vehicle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intestinal tissue
strain: C57BL6/j
treatment: Treated with vehicle
|
| Treatment protocol |
Thirteen-week-old female VillinCreER/0/BrafV600E-LSL/+ mice received either 10 mg/kg atorvastatin by oral gavage or 5% DMSO/PBS vehicle control daily for 12 days. A 20 mg/mL atorvastatin (Generon) stock in DMSO was freshly diluted to a 1 mg/mL working solution in PBS. Days 1-7 of the study were a daily pre-treatment period of atorvastatin/vehicle. Days 8-10 consisted of both atorvastatin/vehicle gavage and intraperitoneal tamoxifen injection to induce BrafV600E expression. On the final day of the study at 3-days post- BrafV600E induction, mice received intraperitoneal injections of 200 μL of 20 mM BrdU solution (Sigma) 3 hrs before tissue harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted on a Promega Maxwell 16 robot using the Maxwell 16 LEV simplyRNA Cells Kit (Reference AS1270). RNA quality and quantity was assessed using the 2100 Bioanalyzer Instrument (Agilent)
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.
|
| |
|
| Hybridization protocol |
Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C . 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) using one color scan setting for 1x44k array slides
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent)
|
| |
|
| Submission date |
Jun 07, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Nicolas Sylvius |
| E-mail(s) |
ns249@le.ac.uk
|
| Organization name |
University of Leicester
|
| Department |
CBS-Genetics
|
| Lab |
Genomic Facility
|
| Street address |
University Road
|
| City |
Leicester |
| ZIP/Postal code |
LE1 1ST |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21810 |
| Series (1) |
| GSE234372 |
BRAFV600E expression in intestinal tissue promotes a cholesterol metabolic gene signature that sustains hyperplasia and characterizes serrated colorectal neoplasia |
|
