run_metadata: 50717
This data as json
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| 50717 | SRR8257205 | SRX5074433 | SRS4088243 | SRP171045 | PRJNA507426 | Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq] | GSE123058 | Transcriptome Analysis | The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants | parent bioproject:PRJNA507423 | pubmed:31296872 | RNAseq in zebrafish wild type embryos at 36hpf replicate 3 | GSM3494529 | tissue:whole embryo|developmental stage:36hpf|genotype:WT | RNAseq in zebrafish wild type embryos at 36hpf replicate 3 | Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene | whole embryo | RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen | Embryos were cultivated at 28°C in E3 medium until desired developmental stage | developmental stage:36hpf|genotype:WT | GSM3494529 | GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq | GSM3494529 | 1 | RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen | GEO Accession:GSM3494529 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP171045 | RNAseq_zebra_WT_36hpf_rep3.fq.gz | fastq | 2560587500.0 | 51211750.0 | GSM3494529 r1 | 0:50 | A:719232941;C:550474431;G:576590260;T:714289868;N:0 | 50 | 719232941 | 550474431 | 576590260 | 714289868 | 0 | SRX5074433 | SRS4088243 | SRA815839 | GEO | CABD/CSIC | 1 | 0.93981 | 0.10951 | 0.71388 | 0.48297 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Spain | 2018-11-28 | Pharyngula | Embryo | Whole Organism | All anatomical structures |