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Series GSE5048 Query DataSets for GSE5048
Status Public on Jan 25, 2007
Title Gene Expression Profiling of Zebrafish Embryonic Retinal Pigment Epithelium in vivo.
Organism Danio rerio
Experiment type Expression profiling by array
Summary Eye development and photoreceptor maintenance requires the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, RPE development has not been studied by a genomic approach. A microarray expression profiling methodology was established in this study for studying RPE development. The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE using microarray and statistical analyses. We found 8810 probesets to be significantly expressed in RPE at 52 hours post-fertilization (hpf), of which 1443 might have biologically meaningful expression levels. Further, 78 and 988 probesets were found to be significantly over- or under-expressed in RPE respectively compared to retina. Also, 79.2% (38/48) of the known over-expressed probesets have been independently validated as RPE-related transcripts. The results strongly suggest that this methodology can obtain in vivo RPE specific gene expression from the zebrafish embryos and identify novel RPE markers.
Keywords: Development, retina, retinal pigment epithelium
 
Overall design The gene expression levels of three independent replicates of retina with RPE attached consisting of ten samples each at 52hpf (WRR52) were compared with three independent pure retinal samples consisting of ten retinas each at 52hpf (WR52). The yield-adjusted WR52 expression values were assumed to be equivalent to the retinal contribution in WRR52 samples and deducted from WRR52 expression values to obtain estimations of RPE gene expression at 52hpf (RPE52). Differential gene expressions between RPE and retina were inferred by comparing the RPE52 estimates and WR52 expression values.
 
Contributor(s) Leung YF, Ma P, Dowling JE
Citation(s) 17251491
Submission date Jun 11, 2006
Last update date Jan 25, 2018
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
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (6)
GSM113854 Wild type retina, 52hpf, pool of ten tissues, biological replicate 1 WR_52hpf_rep1 (WR52_1)
GSM113855 Wild type retina, 52hpf, pool of ten tissues, biological replicate 2 WR_52hpf_rep2 (WR52_2)
GSM113856 Wild type retina, 52hpf, pool of ten tissues, biological replicate 3 WR_52hpf_rep3 (WR52_3)
Relations
BioProject PRJNA96685

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5048_RAW.tar 246.7 Mb (http)(custom) TAR (of CEL, DAT)
Raw data provided as supplementary file

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