Expression Database

GUDMAP:7055

Theiler Stage

Supplemental Data Files

CEL file:	wnt4_mut2.CEL
CHP file:
RPT file:
TXT file:	wnt4_mut2.TXT

Archive ID

Principal Investigator(s)

Andrew P McMahon, Harvard University, Cambridge, MA, USA, amcmahon@med.usc.edu

Submitted By

M Todd Valerius, Harvard University, Cambridge, MA, USA, tvalerius@mcb.harvard.edu

Specimen Details

Sample GEO ID:

GSM144583

Sample Description:

E14.5 whole kidney - Wnt4 null mutant

Title:

wnt4_mut2

Component(s) Sampled:

metanephros (EMAP:6674)

Organism:

Mus musculus

Strain:

129

Genotype:

Non-wild type Allele:
Gene		Wnt4
MGI ID		MGI:1857453
MGI Symbol or lab name
Type		mutant allele
Allele First Chromatid		Wnt4tm1Amc
Allele Second Chromatid		Wnt4tm1Amc
Notes:		PMID: 7990960

Sex:

Unknown

Development Age:

14.5 dpc

Theiler Stage:

Pool Size:

8-10 Wnt4 mutant kidneys (pooled from 4-5 mutant embryos)

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.

Array Hybridization

Extracted Molecule:	total RNA
A260:280 Ratio:	>1.8
RNA Extraction Protocol:	Disruption in liguid nitrogen, total RNA isolation with Qiagen Rneasy, followed by homogenization with QiaShredder columns (two 30ul elutions).
Target Amplification Manufacturer/kit:	Affymetrix (Enzo)
Target Amplification Protocol:	Affymetrix Standard
Rounds of Amplification:	1
Amount Labeled Target Hybridized To Array:	15 ug
Label:	Biotin
Label Protocol:
Array Hyb/Wash Protocol:	EukGE-WS2v4
Scan Protocol:
GCOS Tgt Value:	500
Data Analysis Method:	Affymetrix GCOS and Rosetta Resolver
Reference:	none

Series Details

Series GEO ID:	GSE6288
Number of Samples:	6 samples
Title:	Transcriptional comparison between whole kidneys from E14.5 Wnt4 mutants and wildtype mice (MG_U74Av2 platform). (GUDMAP Series ID: 7)
Summary:	Our laboratory's interest is in understanding the molecular principles that underlie the regional organization of the mammalian metanephric kidney. Our goal is to generate a detailed spatial map of the cellular expression of selected regulatory genes during mammalian kidney development. The goal of this study is to identify a population of genes that are enriched in the renal vesicle (RV) and its derivatives using Wnt4 mutants.
Type:	mutant comparison
Overall 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. Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

Platform Details

Platform GEO ID:	GPL81
Title:	Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Distribution:	commercial
Technology:	in situ oligonucleotide
Organism:	Mus musculus
Manufacturer:	Affymetrix
Manufacturer Protocol:	N/A
Catalogue Number:	N/A