Expression Database

GUDMAP:2192

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

John C Szucsik, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, john.szucsik@cchmc.org

Specimen Details

Sample GEO ID:	GSM108531
Sample Description:	wild-type postnatal day 1 bladder
Title:	43B
Component(s) Sampled:	bladder (EMAP:30374)
Organism:	Mus musculus
Strain:	FVB/N
Genotype:	Wild type
Sex:	Male
Development Age:	P1
Theiler Stage:	27
Pool Size:	N/A
Pooled Sample:	no
Dissection Method:	whole bladder
Experimental Design:	FVB/N female mice are time-mated to control males. Pregnant FVB/N mice are euthanized by standard carbon dioxide asphyxiation. All fetuses and newborn mice are killed by decapitation with a scalpel. Tissues are harvested and used whole or placed in OCT in a mold, frozen and stored at -80°C. Blocks are sectioned, stained and used for laser capture micro-dissection.

Array Hybridization

Extracted Molecule:	total RNA
A260:280 Ratio:	NA
RNA Extraction Protocol:	Qiagen: RNeasy
Target Amplification Manufacturer/kit:
Target Amplification Protocol:	Potter protocols
Rounds of Amplification:	1
Amount Labeled Target Hybridized To Array:	10 ug
Label:	Biotin
Label Protocol:
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:	none

Series Details

Series GEO ID:	GSE4816
Number of Samples:	12 samples
Title:	Gene expression profiles of the P1 bladder isolated from SMAA or SMAGA (Acta2 or Actg2) transgenic and wild type mice. (GUDMAP Series ID: 2)
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 laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing bladder. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing bladder. 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. As a first step we sought to determine if expression of the reporter gene (EGFP or EYFP) used to identify smooth muscle cells altered the gene expression profile of the bladder.
Type:	Comparison of postnatal day 1 bladders.
Overall Design:	Postnatal day 1 bladders were isolated from trangenic and wild-type mice to determine the effects of transgene expression on the gene expression profile in the bladder.

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