|
| Status |
Public on Jul 16, 2012 |
| Title |
Tailbud SU5402 3 hour 3 |
| Sample type |
RNA |
| |
|
| Source name |
tailbud, 3hr, SU5402 treatment, replicate 3
|
| Organism |
Danio rerio |
| Characteristics |
tissue: tailbud
treatment: SU5402
time: 3 h
strain: TLAB
|
| Treatment protocol |
Dechorionated embryos were treated with 0.3M LiCl, 50uM SU5402, or E2 and tailbuds dissected following 3 hours or 7 hours (E2 and SU5402 only).
|
| Growth protocol |
Zebrafish embryos were grown in E2 and at the 4 somite stage chorions were removed and embryos were subjected to chemical treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from dissected tailbuds was extracted using RNA XS (Macherey-Nagel) and cleaned an additional time with RNA Clean and Concentrator kit (Zymo Research). RNA was shipped to Ambry Genetics for labeling, hybridization, and running of the arrays.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amp Labeling Protocol (V.6) (Agilent) according to manufacturor's instructions, followed by RNeasy column purification (Qiagen). Labeling efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| Hybridization protocol |
Labeled cRNA was fragmented and placed on zebrafish 44k whole genome microarray for 17 hours at 65°C.
|
| Scan protocol |
Arrays were washed and scanned at 5uM resolution on an Agilent G2565CA High Resolution Scanner.
|
| Data processing |
Data was processed through Feature Extraction software version 10.7.3.1 using the protocol GE1_107_Sep09 and the 44k grid file 026437_D_F_20091215.
|
| |
|
| Submission date |
Jun 27, 2012 |
| Last update date |
Jul 16, 2012 |
| Contact name |
Michael Jeremy Stulberg |
| Phone |
203-432-3485
|
| Organization name |
Yale University
|
| Department |
MCDB
|
| Lab |
Scott Holley
|
| Street address |
219 Prospect St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL14664 |
| Series (1) |
| GSE38969 |
Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud |
|
