|
| Status |
Public on Jan 01, 2019 |
| Title |
OrgBRAF2_Base BASE |
| Sample type |
RNA |
| |
|
| Source name |
BRAF(2) grown in base media organoid in BASE for 48hr
|
| Organism |
Mus musculus |
| Characteristics |
culture: organoid
|
| Growth protocol |
Male mice from each genotype around the age of 40 days were euthanized by Carbon Dioxide. The first 2.5cm of proximal colon is collected from the mice. The colon crypts were isolated and the culture was established as described previously. Organoids were plated within Matrigel(Corning #356231). Culture media was made of 50% of Wnt3a conditioned media, 20% of R-Spondin conditioned media, 20% of Advanced DMEM/F12(ThermoFisher #12634010) with B27® (ThermoFisher #17504044), 10% of Noggin conditioned media and EGF. The conditioned media for Wnt3a, R-Spondin and Noggin were made as described previously.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA/RNA was extract using Allprep kit mini or micro (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA was generated through in vitro transcription by T7 RNA polymerase in presence of labeled by Cyainine-3 labeled CTP (Perkin Elmer).
|
| |
|
| Hybridization protocol |
825ng of each Cy3- labeled cRNA was hybridized to Agilent mouse GF 4x44K V2 microarray (G4846A) at 65ºC for 17 hours. Then, the arrays were scanned by an Agilent G2565 scanner.
|
| Scan protocol |
Arrays were scanned by an Agilent G2565 scanner.
|
| Data processing |
Expression data were analyzed in the R/Bioconductor environment using the limma package, and quantile normalized.
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
hari easwaran |
| Organization name |
Johns Hopkins University
|
| Department |
Oncology
|
| Lab |
Steve Baylin
|
| Street address |
1650 Orleans Street, CRB1, Room 530
|
| City |
BALTIMORE |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
| |
|
| Platform ID |
GPL10333 |
| Series (2) |
| GSE114800 |
Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [array] |
| GSE114801 |
Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation |
|
