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Expression Database
GUDMAP:13518
Theiler Stage
TS28
Supplemental Data Files
CEL file:
Adult_Capsule_2.CEL
CHP file:
Adult_Capsule_2.rma_gene_default.chp
RPT file:
TXT file:
Adult_Capsule_2.TXT
Archive ID
204
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:
GSM518312
Sample Description:
renal capsule
Title:
Adult_Capsule_2
Component(s) Sampled:
renal capsule (EMAP:29598)
Organism:
Mus musculus
Strain:
CD-1
Genotype:
Wild type
Sex:
male
Development Age:
Adult
Theiler Stage:
28
Pool Size:
1 Adult kidney
Pooled Sample:
No
Dissection Method:
Microdissection
Experimental Design:
Adult CD-1 mice were euthanized by standard carbon dioxide asphyxiation. Kidneys were removed in ice-cold PBS. Using microforceps, the capsule of the kidney was removed and place into an eppendorf tube for RNA isolation.
Array Hybridization
Extracted Molecule:
Total RNA
A260:280 Ratio:
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:
Data Analysis Method:
Affymetrix Expression Console and GeneSpring 10
Reference:
PND 0.5 whole embryo RNA
Series Details
Series GEO ID:
GSE20639
Number of Samples:
3 samples
Title:
Gene expression profiles of adult renal capsule isolated from kidneys using micro-dissection. (GUDMAP Series ID: 36)
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 combination of fluorescent activated cell sorting (FACS) plus 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 FACS 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 capsule cells from the adult kidneys. The capsule cells were isolated from the kidney using microdissection treatment. 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
