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Sample GSM215790 Query DataSets for GSM215790
Status Public on Aug 09, 2007
Title mgb +/- male, E15 bladder (HTM_439)
Sample type RNA
 
Source name HTM_439
Organism Mus musculus
Characteristics mgb +/- male, E15 bladder
Extracted molecule total RNA
Extraction protocol Whole embryos were harvested from timed pregnant females at embryonic day 15 (E15). Embryonic bladders were micro-dissected, snap frozen in liquid nitrogen, and stored at -80C. Bladder tissues were homogenized using a Kontes-pellet pestle (Fisher). High quality total cellular RNA was isolated using the Absolutely RNA Miniprep kit according to the manufacture’s protocol (Stratagene, La Jolla, CA). Sample concentration and purity was determined by optical density 260/280 nm ratios using standard procedures. RNA samples were stored at -80C until further use. Total cellular RNA was extracted from whole embryos by homogenizing samples in TRIzol Reagent as outlined by the supplier (Invitrogen, Carlsbad, CA).
Label biotin
Label protocol standard Affymetrix protocol
 
Hybridization protocol For expression profiling, 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.) and 2.2 µg of cDNA was hybridized per microarray. The microarrays utilized were both obtained from Affymetrix (Santa Clara, CA) and included either the Mouse Genome 430 2.0 GeneChip or the Custom GeneChip Chr11/16. After 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA). GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All steps of sample and microarray processing were performed according to manufacturer's recommendations (Affymetrix, Santa Clara, CA).
Scan protocol standard Affymetrix protocol
Description n/a
Data processing Probe set expression estimates were calculated using WPP algorithm (Auer et al, 2007).
 
Submission date Aug 07, 2007
Last update date Aug 14, 2011
Contact name Kirk M McHugh
E-mail(s) mchughk@ccri.net
Phone 614-355-2817
Organization name Columbus Children's Hospital
Department Cell & Developmental Biology
Street address 700 Children's Drive
City Columbus
State/province OH
ZIP/Postal code 43205
Country USA
 
Platform ID GPL5722
Series (1)
GSE8715 Transcriptional Profiling of the Megabladder Mouse - A Unique Model of Bladder Dysmorphogenesis

Data table header descriptions
ID_REF
VALUE WPP algorithm signal

Data table
ID_REF VALUE
1447886_at 6.403
1422644_at 6.956
1417954_at 9.033
1416935_at 5.832
1447808_s_at 7.647
1449091_at 9.145
1417806_at 6.345
1453352_at 7.126
ENSMUST00000070531_at 3.285
1447493_at 5.95
1455028_at 5.987
1449396_at 7.82
1454866_s_at 6.97
1422580_at 8.241
1419154_at 9.631
1421400_at 6.089
1423227_at 6.233
1449071_at 6.291
1436674_at 5.97
1417928_at 8.198

Total number of rows: 4019

Table truncated, full table size 70 Kbytes.




Supplementary file Size Download File type/resource
GSM215790.CEL.gz 411.9 Kb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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