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Series GSE154895 Query DataSets for GSE154895
Status Public on Feb 22, 2021
Title Rab11a-recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry-Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression, compared to vsx2:Gal4 controls were profiled through bulk RNA-sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated, including activation of Notch-signaling (over-expression of the constitutively active Notch1a intracellular domain; UAS::myc-NICD1a; vsx2::Gal4), activation of Wnt-signaling (over-expression of Wnt2b; UAS::EGFP-Wnt2b;; vsx2::Gal4), activation of Hippo-signaling (over-expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4), and inhibition of mTor signaling (through treatment of zebrafish embryos with Torrin).
 
Overall design 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA-sequencing experiments were performed in triplicate for each experimental condition.
Web link https://0-doi-org.brum.beds.ac.uk/10.3389/fcell.2020.608112
 
Contributor(s) Clark BS, Link BA
Citation(s) 33634099
NIH grant(s)
Grant ID Grant title Affiliation Name
R00 EY027844 Identification of the molecular mechanisms mediating intrinsic control of retinal progenitor competence WASHINGTON UNIVERSITY Brian S Clark
R01 EY014167 Integrative Analyis of Vertebrate Retinal Lamination THE MEDICAL COLLEGE OF WISCONSIN, INC Brian A Link
Submission date Jul 22, 2020
Last update date Mar 02, 2021
Contact name Brian Clark
Organization name Washington University
Department Ophthalmology and Visual Sciences
Lab Clark
Street address 660 S Euclid Ave; Campus Box #8096
City St. Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platforms (1)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
Samples (27)
GSM4681935 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1
GSM4681936 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2
GSM4681937 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3
Relations
BioProject PRJNA647840
SRA SRP273065

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
GSE154895_Normalized_Expression.txt.gz 3.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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