{"database": "metadata", "table": "run_metadata", "rows": [[313, "ERR977398", "ERX1054381", "ERS805482", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R2", "SAMEA3498333", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 2", "unspecified", "1", "Truseq nano DNAsample", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz", "fastq fastq", 17434323262.0, 86308531.0, "ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 2", "0:101 1:101", "A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928", 101, 101, null, null, 5014046305, 3245710338, 3382410145, 5701198546, 90957928, "ERX1054381", "ERS805482", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.87938, 0.83068, 0.30659, 0.31351, 0.80162, 0.8438, 0.50285, 0.47987, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["313"], "units": {}, "query_ms": 5.478890998347197}