run_metadata: 9339
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9339 | ERR2865437 | ERX2871397 | ERS2871017 | ERP111778 | PRJEB29472 | RNAseq analysis of slbp mutants in Zebrafish | ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 | Other | Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. | ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01 | sibling 1 | SAMEA5059846 | Department of Cell and Developmental Biology | ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio | Illumina HiSeq 3000 paired end sequencing | ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 3000 | ERP111778 | Illumina HiSeq 3000 paired end sequencing | ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 | ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz | fastq fastq | 5241628000.0 | 26208140.0 | ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 | 0:100 1:100 | A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601 | 100 | 100 | 1393802799 | 1235804455 | 1219328189 | 1392021956 | 670601 | ERX2871397 | ERS2871017 | ERA1643817 | Department of Cell and Developmental Biology|European Nucleotide Archive | Department of Cell and Developmental Biology | 2 | 0.95296 | 0.95133 | 0.10275 | 0.1028 | 0.67018 | 0.67146 | 0.46488 | 0.46482 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | Unknown | 2018-11-01 | Undetermined | Embryo | Undetermined | Embryo Imprecise |