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Sample GSM215774 Query DataSets for GSM215774
Status Public on Aug 09, 2007
Title mgb +/- male, whole E15 embryo (HT409)
Sample type RNA
 
Source name HT409
Organism Mus musculus
Characteristics mgb +/- male, whole E15 embryo
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
1449986_at 6.963
1417482_at 5.776
1447786_at 5.015
1418266_at 5.312
1421517_at 4.624
1421476_a_at 6.115
1460503_at 4.787
1430557_at 5.375
1458259_x_at 4.565
1420522_at 8.433
1447798_at 4.141
1433106_at 5.513
1433995_s_at 11.417
ENSMUST00000066852_at 7.234
1430261_at 5.989
1458803_at 5.520
1426936_at 2.821
1446687_at 4.765
1438550_x_at 5.285
1425044_at 3.303

Total number of rows: 4019

Table truncated, full table size 70 Kbytes.




Supplementary file Size Download File type/resource
GSM215774.CEL.gz 438.5 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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