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Series GSE101544 Query DataSets for GSE101544
Status Public on Jul 18, 2017
Title Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. These retinal defects can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 days postfertilization (dpf). To capture these initial changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2000 platform. The sequencing analyses indicate that the RNA-Seq dataset was of high quality. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. We found that the fold changes of these genes measured by RT-qPCR highly correlated to those measured by RNA-Seq. Therefore, our RNA-Seq dataset likely captures the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration
Overall design 3 samples of pde6c mutant and 3 samples of wild type animals are analyzed.
Contributor(s) Zhang L, Zhang X, Zhang G, Pang CP, Leung YF, Zhang M, Zhong W
Citation(s) 29231925
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM113242 Novel statistical tools for cell line specific epigenetic analysis UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC Wenxuan Zhong
R01 GM122080 Deciphering the Regulatory Role of Small RNAs on Alternative Splicing UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC PING MA
Submission date Jul 17, 2017
Last update date May 15, 2019
Contact name Nadejda Beliakova-bethell
Organization name University of California San Diego
Street address 9500 Gilman Dr, La Jolla
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
Samples (6)
GSM2705944 wild type retina sample 1 (WR1)
GSM2705945 wild type retina sample 2 (WR2)
GSM2705946 wild type retina sample 3 (WR3)
BioProject PRJNA394760
SRA SRP112616

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

Supplementary file Size Download File type/resource
GSE101544_cts-wgtf-gene2-upload.txt.gz 627.5 Kb (ftp)(http) TXT
GSE101544_genes.fpkm_table_upload.txt.gz 580.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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