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Sample GSM279686 Query DataSets for GSM279686
Status Public on Sep 15, 2008
Title SmoGli3_L
Sample type RNA
 
Source name Age: E11.5 Forelimbs
Organism Mus musculus
Characteristics Age: E11.5 Forelimbs
Growth protocol Mouse forelimbs dissected from day 11.5 mouse embryos
Extracted molecule total RNA
Extraction protocol Shh mutant phenotypes were manually identified as wild-type or mutants. All other samples were snap frozen in liquid N2 and genotyped. Either single or dual samples of equivalent genotyped samples (2-4 forelimbs) were used for all other samples. All samples contained 5μg of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinus™ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).
Label biotin
Label protocol Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G
Description Smo and Gli3 double knock-out limb bud at E11.5, biological rep3
Forelimbs from embryo 1006 (Gli3-/-;Smo n/c) double mutant
Data processing Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
 
Submission date Apr 04, 2008
Last update date Jan 29, 2022
Contact name Steven A. Vokes
E-mail(s) svokes@austin.utexas.edu
Organization name University of Texas at Austin
Department Molecular Biosciences
Street address 2500 Speedway, STOP A5000
City Austin
State/province Texas
ZIP/Postal code 78757
Country USA
 
Platform ID GPL6096
Series (2)
GSE11063 Expression data from E11.5 mouse embryonic forelimbs - various mutant conditions or dissected limb domains
GSE11077 A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb

Data table header descriptions
ID_REF
VALUE Quantile normalized gene level expression values.

Data table
ID_REF VALUE
6747308 674.407607
6747309 1470.327683
6747314 730.269922
6747326 2.784741
6747343 295.507103
6747354 7.145327
6747364 440.674926
6747471 510.435903
6747472 14.877921
6747478 4.149378
6747497 260.488884
6747504 24.648706
6747515 456.115061
6747577 13.367817
6747641 233.503603
6747696 4.154714
6747747 1014.639137
6747786 671.889419
6747805 217.911421
6747837 566.262821

Total number of rows: 17213

Table truncated, full table size 309 Kbytes.




Supplementary file Size Download File type/resource
GSM279686.CEL.gz 20.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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