run_metadata: 67094
This data as json
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| 67094 | SRR17055694 | SRX13244623 | SRS11168042 | SRP348277 | PRJNA784298 | Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] | GSE189737 | Transcriptome Analysis | Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. | parent bioproject:PRJNA784293 | pubmed:37227126 | WT 1 | GSM5706504 | tissue:head|developmental stage:18 hpf|genotype:WT | WT 1 | Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output | head | Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA | zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage | developmental stage:18 hpf|genotype:WT | GSM5706504 | GSM5706504: WT 1; Danio rerio; RNA Seq | GSM5706504 | 1 | Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA | GEO Accession:GSM5706504 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP348277 | 180309_SNK268_B_L006_AJSG-7_R1.fastq.gz 180309_SNK268_B_L006_AJSG-7_R2.fastq.gz | fastq fastq | 12083337300.0 | 40277791.0 | GSM5706504 r1 | 0:150 1:150 | A:3379986050;C:2659960500;G:2767236627;T:3274019596;N:2134527 | 150 | 150 | 3379986050 | 2659960500 | 2767236627 | 3274019596 | 2134527 | SRX13244623 | SRS11168042 | SRA1335663 | GEO | IRCSS-SDN | 2 | 0.89628 | 0.8988 | 0.32007 | 0.31887 | 0.70899 | 0.71246 | 0.45974 | 0.46528 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | rrna_depletion | ribozero | bulk | unknown | unknown | Italy | 2021-11-28 | Segmentation | Embryo | Head | Nervous System |