Expression Database

GUDMAP:10724

Theiler Stage

Supplemental Data Files

Archive ID

Principal Investigator(s)

James Lessard, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, james.lessard@cchmc.org

Submitted By

Alfor Lewis, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, alfor.lewis@cchmc.org

Specimen Details

Sample GEO ID:	GSM315976
Sample Description:	embryonic day 13 bladder mesenchyme cells
Title:	mesenchyme2
Component(s) Sampled:	mesenchymal layer of primitive bladder (EMAP:30878)
Organism:	Mus musculus
Strain:	FVB/N
Genotype:	Wild type
Sex:	Unknown
Development Age:	13 dpc
Theiler Stage:	21
Pool Size:	NA
Pooled Sample:	no
Dissection Method:	Bladder microdissected and treated with 20 µM EDTA to dissociate the mesenchyme from the epithelium.
Experimental Design:	FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were micro-dissected, cut just above the ureters and treated with 20µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

Array Hybridization

Extracted Molecule:	total RNA
A260:280 Ratio:	NA
RNA Extraction Protocol:	Qiagen:RNEASY
Target Amplification Manufacturer/kit:	TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplification Protocol:	Potter Protocols
Rounds of Amplification:	2
Amount Labeled Target Hybridized To Array:	10ug
Label:	Biotin
Label Protocol:	Biotin-X-X-NHS (EPICENTRE Biotechnologies)
Array Hyb/Wash Protocol:	Affymetrix standard protocol
Scan Protocol:
GCOS Tgt Value:	1500
Data Analysis Method:	Affymetrix GCOS and Gene Spring and Avadis programs
Reference:	NA

Series Details

Series GEO ID:	GSE12618
Number of Samples:	6 samples
Title:	Gene expression profiles of E13 bladder compartments. (GUDMAP Series ID: 24)
Summary:	The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the e13 mouse bladder.
Type:	Mouse embryonic day 13 bladder mesenchyme and epithelium.
Overall Design:	FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected, cut just above the ureters, and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip

Platform Details

Platform GEO ID:	GPL1261
Title:	Affymetrix GeneChip Mouse Genome 430 2.0 Array
Distribution:	commercial
Technology:	in situ oligonucleotide
Organism:	Mus musculus
Manufacturer:	Affymetrix
Manufacturer Protocol:	N/A
Catalogue Number:	N/A