|
Status |
Public on Jan 03, 2014 |
Title |
YR_52hpf_rep2 |
Sample type |
RNA |
|
|
Source name |
Young (smarca4) mutant retina, 52hpf, pool of nine tissues
|
Organism |
Danio rerio |
Characteristics |
strain: AB genotype: young (smarca4) age: 52hpf tissue: Retina
|
Treatment protocol |
The tissues were dissected from developing embryos according to: Zhang L, Leung YF. Microdissection of zebrafish embryonic eye tissues. J Vis Exp. 2010;(40). doi:pii: 2028. Then, the tissues were pooled as one biological replicate. 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.
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Scan protocol |
Scanning was done according to a standard procedure from Affymetrix.
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Description |
Young (smarca4) mutant retina, 52hpf, pool of nine tissues, biological replicate 2
|
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.
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|
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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 |
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