run_metadata: 43421
This data as json
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| 43421 | SRR5931501 | SRX3091759 | SRS2429122 | SRP115384 | PRJNA398194 | Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and Wwtr1 | GSE102606 | Transcriptome Analysis | The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior posterior axis during the somite forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord and play a critical and unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord. We also find that Yap1/Wwtr1 also acting through Fibronectin have an essential role in the ectodermal morphogenesis necessary to form the initial dorsal and ventral fins a process that had been thought to involve bending of an epithelial sheet but which we now show involves active cell migration. Our results reveal how the Hippo pathway transcriptional program localized to two specific tissues acts to control essential morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings 24 each at 16 18 somite stage were collected for RNAseq. Tails are tissues of the posterior end until the third newest somite S III. | pubmed:29283341 | mutants replicate1 | GSM2741692 | source name:tails|developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants | mutants replicate1 | Reads trimming: Trimmomatic v0.33 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15 Alignment: STAR 2.4.0a outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 30 outFilterMultimapNmax 999 alignEndsProtrude 10 ConcordantPair normalization and statistics: Cufflinks suite v2.2.1 standard parameters Genome build: Zv10 Supplementary files format and content: fpkm tracking | tails | RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit | developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants | GSM2741692 | GSM2741692: mutants replicate1; Danio rerio; RNA Seq | GSM2741692 | 1 | RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit | GEO Accession:GSM2741692 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP115384 | jason_tail_mut2_R1.fastq jason_tail_mut2_R2.fastq | fastq fastq | 1330843114.0 | 8934569.0 | GSM2741692 r1 | 0:74.53 1:74.43 | A:334692975;C:325256311;G:332297545;T:338565318;N:30965 | 74 | 74 | 334692975 | 325256311 | 332297545 | 338565318 | 30965 | SRX3091759 | SRS2429122 | SRA598978 | GEO | Stainier Lab, Developmental Genetics, Max Planck Institute For Heart and Lung Research | 2 | 0.96799 | 0.96959 | 0.07645 | 0.07614 | 0.72115 | 0.72508 | 0.48043 | 0.48512 | 75 | 75 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2017-08-14 | Undetermined | Embryo | Trunk | Surface Structure |