|
| Status |
Public on Feb 03, 2007 |
| Title |
wnt4_430_wt1 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type kidney
|
| Organism |
Mus musculus |
| Characteristics |
gene reported: wild-type
strain: CD-1
sex: unknown
developmental stage: E14.5
theiler stage: 22
somite count: NA
developmental landmark: NA
|
| Treatment protocol |
pool size: 2 wild-type kidneys
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction. Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants. At E14.5, these structures are present in wildtype kidneys. Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates. CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug. Presence of a plug is taken as day 0.5 post coitum. Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are euthanized by decapitation with scissors. Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Disruption in liguid nitrogen, total RNA isolation with Qiagen Rneasy, followed by homogenization with QiaShredder columns (two 30ul elutions).
|
| Label |
Biotin
|
| Label protocol |
Affymetrix standard protocol
|
| |
|
| Hybridization protocol |
Amount labeled target hybridization to array: 15 ug
Hybridization/Wash/Stain protocol: EukGE-WS2v4_450
|
| Scan protocol |
Affymetrix standard protocol
|
| Description |
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7165
|
| Data processing |
Analysis method: Affymetrix GCOS and Rosetta Resolver GCOS Tgt value: 500
|
| |
|
| Submission date |
Feb 01, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
GUDMAP Developers |
| E-mail(s) |
gudmap-db@gudmap.org
|
| Phone |
+44 131 651 8500
|
| Organization name |
IGMM MRC Human Genetics Unit
|
| Lab |
GUDMAP Database Group
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE6934 |
Transcriptional comparison between whole kidneys from E14.5 Wnt4 mutants and wildtype mice (Mouse430_2 platform). (GUDMAP Series ID: 13) |
|
| Relations |
| Reanalyzed by |
GSE119085 |
