Expression Database

GUDMAP:12335

Theiler Stage

Images

Supplemental Data Files

CEL file:	Adult_Whole_Glom_3.CEL
CHP file:	Adult_Whole_Glom_3.rma_gene_default.chp
RPT file:	NA
TXT file:	Adult_Whole_Glom_3.TXT

Archive ID

Principal Investigator(s)

Steve Potter, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, steve.potter@cchmc.org

Submitted By

Eric Brunskill, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, brune0@cchmc.org

Specimen Details

Sample GEO ID:	GSM429037
Sample Description:	Adult Renal Corpusle
Title:	Adult_Whole_Glom_3
Component(s) Sampled:	mature renal corpuscle (EMAP:29525)
Organism:	Mus musculus
Strain:	CD-1
Genotype:	Wild type
Sex:	Male
Development Age:	Adult
Theiler Stage:	28
Pool Size:	approx 2 Adult Kidney
Pooled Sample:	Yes
Dissection Method:	Renal corpuscles were isolated using a combination of Collagenase A digestion and sieving.
Experimental Design:	7-9 week old adult male mice were euthanized by standard carbon dioxide asphyxiation. The kidneys were isolated and placed in ice-cold PBS. The kidneys were minced with a razor blade and incubated in the presence of 300 µl of 0.5% Collagenase A for 15 minutes at 37 ºC. After incubation, the kidneys were further dissociated by titurating in the presence of 600 µl of ice-cold 10% FBS/PBS, and then pelleted at 5000 rpm, 4 ºC for 5 minutes. The cells were resuspended in 500 µl of ice-cold 2% FBS/PBS. Mature renal corpuscles were isolated using a decreasing series of filter sizes (100µm, 70 µm, 40 µm).

Array Hybridization

Extracted Molecule:	Total RNA
A260:280 Ratio:	NA
RNA Extraction Protocol:	Potter protocol: 'RNA purification'
Target Amplification Manufacturer/kit:	WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplification Protocol:	Potter protocols
Rounds of Amplification:	1
Amount Labeled Target Hybridized To Array:	2.5µg
Label:	Biotin
Label Protocol:	The FL-Ovation cDNA Biotin Module V2 (NuGEN)
Array Hyb/Wash Protocol:	Affymetrix Standard Protocol. The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilising the fluidics protocol FS450-0007.
Scan Protocol:	Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4.
GCOS Tgt Value:	NA
Data Analysis Method:	Affymetrix Expression Console and GeneSpring 10
Reference:	PND 0.5 whole embryo RNA

Series Details

Series GEO ID:	GSE17141
Number of Samples:	3 samples
Title:	Gene expression profiles of adult renal corpusle isolated using sieving techniques. (GUDMAP Series ID: 30)
Summary:	The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The use of microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in isolated components of the developing kidney. 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.
Type:	Expression profiling of kidney components by microarray
Overall Design:	CD-1 mice were utilized to isolate the renal corpusle from the kidneys of adult mice. The renal corpusle were isolated from the kidney using a sieving procedure. RNA was isolated and the gene expression profiles were determined by microarrays.

Platform Details

Platform GEO ID:	GPL6246
Title:	Affymetrix Mouse Gene 1.0 ST Array
Distribution:	commercial
Technology:	in situ oligonucleotide
Organism:	Mus musculus
Manufacturer:	Affymetrix
Manufacturer Protocol:	N/A
Catalogue Number:	N/A