|
| Status |
Public on Sep 15, 2008 |
| Title |
Shh_Mut_A |
| Sample type |
RNA |
| |
|
| Source Name |
Genotype Shh -/-
|
| Organism(s) |
Mus musculus |
| Characteristics |
Age: E11.5 Forelimbs, Genotype Shh -/-
|
| 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 |
Shh loss-of-function mutant limb bud at E11.5, biological rep1
Forelimbs from Shh mutants 946 and 947
|
| 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 |
| Contact name |
Steven A. Vokes |
| Organization name |
Harvard University
|
| Department |
Molecular & Cellular Biology
|
| Lab |
Andy McMahon
|
| Street address |
16 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| 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 |
|
