run_metadata: 67761
This data as json
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| 67761 | SRR17267991 | SRX13446017 | SRS11345216 | SRP351480 | PRJNA790108 | Shutdown corner a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish | PRJNA790108 | Other | Morphogenesis the formation of three dimensional organ structures requires precise coupling of genetic regulation and complex cell behaviors. The genetic networks governing many morphogenetic systems including that of the embryonic eye are poorly understood. In zebrafish several forward genetic screens have sought to identify factors regulating eye development. These screens often look for eye defects at stages post the optic cup is formed and when retinal neurogenesis is under way. This approach can make it difficult to identify mutants specific for morphogenesis as opposed to neurogenesis. To this end we carried out a forward genetic small scale haploidmutagenesis screen in zebrafish Danio rerio to identify factors that govern optic cup morphogenesis. We screened 100 genomes and isolated shutdown corner sco a mutant which exhibits multiple tissue defects and harbors a 10 Mb deletion that encompasses 89 annotated genes. Using a combination of live imaging and antibody staining we found cell proliferation cell death and tissue patterning defects in the sco optic cup. We also observed other phenotypes including paralysis neuromuscular defects and ocular vasculature defects. To date the largest deletion mutants reported in zebrafish are engineered using CRISPR Cas9 and are less than 300 kb. Because of the number of genes within the deletion interval shutdown corner DfChr05:scoz207 could be a useful resource to the zebrafish community as it may be helpful for gene mapping understanding genetic interactions or for study of the many genes lost in the mutant. | sco Mutant | strain:AB|age:3 dpf|sex:pooled male and female|tissue:whole embryo|genotype:Homozygous Mutant|BioSampleModel:Model organism or animal | RNA Seq of Zebrafish Embryos: 3 dpf sco mutant | 8525X1 | 8525X1 | Sequencing libraries 18 pM were chemically denatured and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina TruSeq SR Cluster Kit v3 cBot HS GD 401 3001. Following transfer of the flowcell to an Illumina HiSeq 2500 instrument HCS v2.0.12 and RTA v1.17.21.3 a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents FC 401 3002. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP351480 | 8525X1_111104_SN141_0409_BD0DR0ABXX_1.txt | fastq | 2385441300.0 | 47708826.0 | 8525X1 111104 SN141 0409 BD0DR0ABXX 1.txt | 0:50 | A:625043248;C:578161916;G:551073234;T:630745508;N:417394 | 50 | 625043248 | 578161916 | 551073234 | 630745508 | 417394 | SRX13446017 | SRS11345216 | SRA1345457 | Brigham Young University|Physiology and Developmental Biology | University of Utah | 1 | 0.93674 | 0.06315 | 0.67919 | 0.4512 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2021-12-18 | Larval | Larval | Whole Organism | All anatomical structures |