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Expression Database
GUDMAP:11677
Theiler Stage
TS21
Supplemental Data Files
CEL file:
L_081308_UE1_13_MOE430_2.CEL
CHP file:
L_081308_UE1_13_MOE430_2.CHP
RPT file:
L_081308_UE1_13_MOE430_2.RPT
TXT file:
L_081308_UE1_13_MOE430_2.TXT
Archive ID
163
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:
GSM396511
Sample Description:
embryonic day 13 bladder neck/urethral epithelial cells
Title:
urothelium1_200209
Component(s) Sampled:
epithelial layer of primitive bladder (EMAP:30875)
Organism:
Mus musculus
Strain:
FVB/N
Genotype:
Wild type
Sex:
Unknown
Development Age:
13 dpc
Theiler Stage:
21
Developmental Landmark:
embryonic day 13
Pool Size:
NA
Pooled Sample:
no
Dissection Method:
Bladder neck/urethra microdissected by cutting the specimen at the level of ureter insertion and treated with 1 mg/ml trypsin in Tyrode's solution 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 1 mg/ml trypsin in Tyrode's solution for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder neck with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
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:
GSE15794
Number of Samples:
6 samples
Title:
Gene expression profiles of E13 bladder neck/urethral compartments. (GUDMAP Series ID: 25)
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 micro dissected 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 neck/urethral compartment.
Type:
Mouse embryonic day 13 bladder neck/urethral 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 and cut just below the ureters. Since the EDTA dissociation was ineffective, the bladder neck and urethra were collected and treated with 1 mg/ml trypsin in Tyrode's solution for 20 minutes at 37 deg C. The layers were separated using a fine needle and rimming. The samples were placed in RLT and stored at -80 deg C. RNA was prepared and the Epicenter 2-round amplification scheme described under the Lessard Group Protocols on the GUDMAP pages were performed. The amplified RNA was examined with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
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
