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Sample GSM429023 Query DataSets for GSM429023
Status Public on Jul 16, 2010
Title CRYM_P1
Sample type RNA
 
Source name cap mesenchyme
Organism Mus musculus
Characteristics gene reported: Tg(Crym-EGFP)82Gsat / MMRRC:012003-UCD
strain: CD-1
sex: unknown
developmental stage: P1
theiler stage: TS27
somite count: NA
developmental landmark: NA
Treatment protocol pool size: approx 4 P1 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated. Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation. Neonatal pups were fostered to new CD-1 females. At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS. The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC. After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes. The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.
Extracted molecule total RNA
Extraction protocol Potter protocol: 'RNA purification'
Label Biotin
Label protocol The FL-Ovation cDNA Biotin Module V2 (NuGEN) is used to chemically modify fragments and label target sense cDNA.
 
Hybridization protocol Affymetrix standard protocol
Amount labeled target hybridization to array: 2.5 µg
The arrays were washed and and stained using a Fluidics Station 450 (Affymetrix) utilizing 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.
Description >> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12315
Data processing Analysis method: Affymetrix Expression Console and GeneSpring 10.
 
Submission date Jul 16, 2009
Last update date Dec 31, 2010
Contact name GUDMAP Developers
E-mail(s) [email protected]
Phone +44 131 651 8500
Organization name IGMM MRC Human Genetics Unit
Lab GUDMAP Database Group
Street address Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platform ID GPL6246
Series (2)
GSE17139 Gene expression profiles of cap mesenchyme and renal vesicle isolated between P0-P4 from Crym-EGFP neonatal transgenic mice using FACS. (GUDMAP Series ID: 28)
GSE17218 Encyclopedia of the expression levels of all genes in multiple components of the developing kidney

Data table header descriptions
ID_REF
VALUE RMA signal intensity (log2)

Data table
ID_REF VALUE
10338001 12.61352
10338002 6.03269
10338003 11.47589
10338004 10.52379
10338005 2.90190
10338006 3.11105
10338007 3.44184
10338008 4.19274
10338009 6.92534
10338010 2.96061
10338011 5.70954
10338012 3.02177
10338013 2.80821
10338014 2.85291
10338015 2.80380
10338016 6.73226
10338017 13.01119
10338018 6.51264
10338019 5.29735
10338020 7.25887

Total number of rows: 35557

Table truncated, full table size 592 Kbytes.




Supplementary file Size Download File type/resource
GSM429023.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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