|
| Status |
Public on Aug 18, 2010 |
| Title |
IM4_SPT |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish Intermediate Mesoderm 4/5-somite stage
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 4/5-somite
genotype: spt/tbx16 mutant
|
| Treatment protocol |
No treatments were given to the fish -- comparisons were made between wild-type and mutant individuals. Mutants harbored the b104 mutant allele of the transcription factor tbx16/spt.
|
| Growth protocol |
Fish were grown and cared for following standard techniques (Westerfield M: The zebrafish book: a guide for the laboratory use of zebrafish (Danio rerio): University of Oregon Press Eugene, OR; 1995)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA (amplified using two rounds of RNA amplification carried out using the RiboAmp HS RNA Amplification Kit (Arcturus)). RNA was extracted using the PicoPure isolation kit (Arcturus)
|
| Label |
biotin
|
| Label protocol |
Biotin following standard Affymetrix protocols by the University of Chicago functional genomics core facility
|
| |
|
| Hybridization protocol |
Following standard Affymetrix protocols by the University of Chicago functional genomics core facility
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from 4/5-somite stage intermediate mesoderm
|
| Data processing |
Image acquisition and initial array quantification were performed using the Affymetrix Microarray Suite Version 5.0. Subsequent identification of differentially expressed genes between wild-type and mutant tissue was performed using dCHIP with invariant set normalization.
|
| |
|
| Submission date |
Jan 20, 2010 |
| Last update date |
Aug 18, 2010 |
| Contact name |
Rachel Lockridge Mueller |
| E-mail(s) |
rlm@colostate.edu
|
| Phone |
(970) 491-6717
|
| Organization name |
Colorado State University
|
| Department |
Biology
|
| Street address |
1878 Campus Delivery
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523-1878 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE19955 |
Expression data comparing wild-type and spt mutant zebrafish tissues at two developmental time points. |
|
