{
  "metaData" : {
    "dateProduced" : "2026-04-13T22:34:26-07:00",
    "dataProvider" : {
      "crossReference" : {
        "id" : "ZFIN",
        "pages" : [ "homepage" ]
      },
      "type" : "curated"
    }
  },
  "data" : [ {
    "title" : "High-throughput sequencing of mRNA from oocyte, 1 cell, 16/32 cells, 128/256 cells, 3.5hpf and 5.3hpf zebrafish embryos (Wild type; AB line)",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-1",
      "alternateIds" : [ "GEO:GSE22830" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE22830",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-110523-20",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:21555364"
    }, {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-140429-1",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:24586560"
    }, {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-130611-13",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:23676078"
    } ],
    "summary" : "mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un-annotated regions of the genome, as well as splice variants with an estimated frequency of 40-75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies, gene discovery, and genome annotation.",
    "categoryTags" : [ "developmental time course", "baseline" ]
  }, {
    "title" : "[E-MTAB-434] Transcription profiling by high throughput sequencing of zebra fish tissues and developmental stages",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-2",
      "alternateIds" : [ "GEO:GSE30603" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE30603",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-120718-36",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:22798491"
    } ],
    "summary" : "Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages using the Illumina Genome Analyzer. Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues and developmental stages using the Illumina Genome Analyzer. These data have been used to improve the gene annotation of the zebrafish genome. Study description: Zebrafish total RNA was extracted from embryonic and adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 36, 37, 54 and 76 base reads on the Illumina Genome Analyzer.",
    "categoryTags" : [ "developmental time course", "sex", "tissue type study", "baseline" ]
  }, {
    "title" : "[E-MTAB-460] Sanger_zebrafish_sequencing",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-3",
      "alternateIds" : [ "GEO:GSE30608" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE30608",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-110907-26",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:21887364"
    } ],
    "summary" : "Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer.",
    "categoryTags" : [ "tissue type study", "baseline" ]
  }, {
    "title" : "RNA-sequencing project for zebrafish embryo and larva development",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-4",
      "alternateIds" : [ "GEO:GSE45706" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE45706",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-130703-15",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:23700457"
    }, {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-160219-3",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:26891128"
    } ],
    "summary" : "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. We sequenced the polyA-extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development.",
    "categoryTags" : [ "developmental time course", "baseline" ]
  }, {
    "title" : "Transcriptomic analysis of zebrafish during development and homeostasis",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-5",
      "alternateIds" : [ "GEO:GSE39703" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE39703",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-130611-31",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:23684812"
    } ],
    "summary" : "Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end (16-36 hpf, 5 day larvae, adult head and adult tail) or paired end (24 hpf) libraries (Illumina). Single end reads of 36 nucleotides and paired end reads (2 x 76 nucleotides) were obtained with a GAIIx (Illumina). Gene expression at the different stages/tissu was assessed by cufflinks and HTseq.",
    "categoryTags" : [ "developmental time course", "tissue type study", "baseline" ]
  }, {
    "title" : "RNA sequencing of the developing zebrafish head",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-6",
      "alternateIds" : [ "GEO:GSE63191" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE63191",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-150107-3",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:25561519"
    } ],
    "summary" : "We sequenced strand-specific mRNA from the heads of 3 groups of wild type zebrafish (Danio rerio) 5 days post fertilization.",
    "categoryTags" : [ "tissue type study", "baseline" ]
  }, {
    "title" : "Neurotranscriptome profiles of four zebrafish strains",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-7",
      "alternateIds" : [ "GEO:GSE61108" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE61108",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-141019-5",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:25326170"
    }, {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-150603-7",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:26032017"
    }, {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-150827-1",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:26309813"
    } ],
    "summary" : "Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex-specific behavioral variation particulary in response to stress and anxiety-inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish, this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA-sequencing (4 biological replicates per strain further subdivided into 2 biological replicates per sex) we analyzed the whole-brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences (e.g. behavioral or morphological) of the strains. Using a balanced block design, all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads (approximately 52 million reads per biological replicate) were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic (e.g. morphological, behavioral) variation in zebrafish.",
    "categoryTags" : [ "sex", "tissue type study", "baseline" ]
  }, {
    "title" : "Transcriptome profiling from the brain of male and female zebrafish",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-8",
      "alternateIds" : [ "GEO:GSE67092" ],
      "preferredCrossReference" : {
        "id" : "GEO:GSE67092",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-160605-5",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:27259666"
    } ],
    "summary" : "Genome-wide analysis to identify sex specific transcripts in the brain of male and female zebrafish",
    "categoryTags" : [ "sex", "tissue type study", "baseline" ]
  }, {
    "title" : "Baseline expression from transcriptional profiling of zebrafish developmental stages",
    "datasetId" : {
      "primaryId" : "ZFIN:ZDB-HTPDSET-200812-9",
      "alternateIds" : [ "ArrayExpress:E-ERAD-475" ],
      "preferredCrossReference" : {
        "id" : "GEO:E-ERAD-475",
        "pages" : [ "htp/dataset" ]
      }
    },
    "dateAssigned" : "2020-08-12T15:50:43-07:00",
    "publications" : [ {
      "crossReference" : {
        "id" : "ZFIN:ZDB-PUB-171117-18",
        "pages" : [ "reference" ]
      },
      "publicationId" : "PMID:29144233"
    } ],
    "summary" : "Establish baseline expression transcriptional signatures for zebrafish developmental stages. Total RNA was extracted from single wild type zebrafish embryos at a series of different developmental stages. RNA from 12 embryos was pooled to generate a replicate.The RNA was DNase treated. Stranded RNAseq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",
    "categoryTags" : [ "developmental time course", "baseline" ]
  } ]
}