|
| Status |
Public on Nov 21, 2015 |
| Title |
Veh rep1 |
| Sample type |
RNA |
| |
|
| Source name |
KP mice_vehicle
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: KP orthotopic tumor-bearing mice
gender: female
age: 8 weeks
treated with: vehicle for 14 days
|
| Treatment protocol |
We treated KP orthotopic tumor-bearing mice with vehicle and FAKi (50mg/kg) by gavage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tumor tissues of KP tumor-bearing mice treated with vehicle and FAKi was isolated using NucleoSpin Kit according to the manufacturer's instruction.
|
| Label |
Cy5
|
| Label protocol |
Cyanine-5 (Cy5) 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 |
1.5 ug of Cy5-labelled cRNA (specific activity >10.0 pmol Cy5/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 Mouse 8x60K Expression Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. 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 8x60K array slides (Scan resolution 10um, Red Dye channel, PMT 100%).
|
| Description |
534-18534-Veh
|
| Data processing |
Raw data values were log2-transformed and quantile normalized across all samples. Detectable genes were defined as those with a detected call in at least 10% of samples studied. R software package “limma” was used to detect differentially expressed genes. Significant genes were determined at p<0.05 and absolute fold-change >=1.5.
|
| |
|
| Submission date |
Nov 20, 2015 |
| Last update date |
Nov 21, 2015 |
| Contact name |
David DeNardo |
| E-mail(s) |
DDENARDO@DOM.wustl.edu
|
| Organization name |
Washington University in St. louis
|
| Street address |
425 S. Euclid Avenue
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE75233 |
Targeting Focal Adhesion Kinase Renders Pancreatic Cancers Responsive to Checkpoint Immunotherapy |
|
