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Sample GSM215772 Query DataSets for GSM215772
Status Public on Aug 09, 2007
Title Wild type female, whole E15 embryo (F384)
Sample type RNA
 
Source name F384
Organism Mus musculus
Characteristics wild type female, 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
1419226_at 5.063
1447785_x_at 5.047
1440480_at 7.382
1441035_at 2.598
ENSMUST00000066852_at 5.894
1458347_s_at 4.467
1420523_at 5.258
1453540_at 3.385
1442582_at 3.000
1431755_a_at 3.943
1449698_at 3.274
1431072_a_at 7.822
1420522_at 7.136
1430658_a_at 2.271
1449497_at 5.599
1455766_at 6.102
1450751_at 3.804
1417859_at 3.128
1433311_at 3.176
1433995_s_at 10.095

Total number of rows: 4019

Table truncated, full table size 70 Kbytes.




Supplementary file Size Download File type/resource
GSM215772.CEL.gz 468.8 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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