|
| Status |
Public on Jun 21, 2016 |
| Title |
WNT11_DMZ_1 |
| Sample type |
RNA |
| |
|
| Source name |
Dorsal marginal zone explants, WNT11MO injected
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Dorsal marginal zone explants
developmental stage: Stage 12
|
| Treatment protocol |
DMZ explants were dissected at stage 10.25 and cultivated until their siblings reach stage 12
|
| Growth protocol |
Xeopus laevis were injected in both dorsal blastomeres at 8-cell stage (COMO, WNT5AMO, WNT11MO) and cultivated until stage 10.25
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 30 DMZ explants via TRIzol Plus RNA Purification Kit (Life Technologies GmbH, Germany) according to manufactur's instructions. Total RNA was concentrated by Rneasy MinElute Cleanup Kit (Qiagen, Germany). Only probes with a RIN-value over 8 were used for the analysis (Agilent 2100 Bioanalyzer)
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit, One Colour (Agilent) according to the manufacturer's instructions, purification by RNAeasy Mini Kit (Qiagen, Germany). Dye incorporation and cRNA yield were checked with a Spectrophotometer.
|
| |
|
| Hybridization protocol |
at least 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the Gene Expression Hybridization Kit (Agilent). The probes were hybridized to a Xenopus 4x44K gene expression chip (Agilent) for 17 h at 65°C. After hybridization, the chips were washed.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.
|
| Description |
Stage 12 dorsal marginal zone explants, WNT11MO injected
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (Version 10.7.3.1, Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 023448_D_F_20130122) to obtain background and spatially detrended processed signal intensities. The raw data were quantile normalized and afterwards log2-transformed with the aid of the Bioconductor R software.
|
| |
|
| Submission date |
May 26, 2016 |
| Last update date |
Jun 21, 2016 |
| Contact name |
Dietmar Gradl |
| Organization name |
Karlsruhe Institute of Technology
|
| Street address |
Fritz Haber Weg 2
|
| City |
Karlsruhe |
| ZIP/Postal code |
76131 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17215 |
| Series (1) |
| GSE81924 |
Identification of specific xWNT5A and xWNT11specific target genes in dorsal marginal zone explants of Xenopus laevis |
|
