|
| Status |
Public on Jan 03, 2014 |
| Title |
WA_52hpf_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Wild type whole embryo, 52hpf, pool of ten embryos
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
genotype: Wild-type
age: 52hpf
tissue: Whole embryo
|
| Treatment protocol |
Ten embryos were collected according to: Leung YF, Ma P, Link BA, Dowling JE. Factorial microarray analysis of zebrafish retinal development. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12909-14. Then, the samples were pooled as one biological replicate. The young (smarca4) mutants were staged by staging their wild-type siblings.
see sample section
|
| Growth protocol |
Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.
|
| Label |
Biotin
|
| Label protocol |
Affymetrix GeneChip Two-Cycle Target Labeling protocol.
|
| |
|
| Hybridization protocol |
Hybridization, washing and staining were done according to a standard procedure from Affymetrix.
|
| Scan protocol |
Scanning was done according to a standard procedure from Affymetrix.
|
| Description |
Wild type whole embryos, 52hpf, pool of ten embryos, biological replicate 3
|
| Data processing |
The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7 (http://www.bioconductor.org), running in the R statistical environment version 2.2.0 (http://www.r-project.org) using default parameters.
|
| |
|
| Submission date |
Aug 27, 2013 |
| Last update date |
Jan 04, 2014 |
| Contact name |
Yuk Fai Leung |
| E-mail(s) |
yfleung@purdue.edu
|
| Phone |
765-496-3153
|
| Organization name |
Purdue University
|
| Department |
Biological Sciences
|
| Lab |
Leung
|
| Street address |
915 W. State Street
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE50241 |
Expression profiling of the retinal pigment epithelium in zebrafish smarca4 mutant |
|
