{"database": "metadata", "table": "run_metadata", "rows": [[51207, "SRR8587728", "SRX5388267", "SRS4376706", "SRP186180", "PRJNA523009", "Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq", "GSE126701", "Transcriptome Analysis", "Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema  a mass of proliferative cells that can grow and develop into the lost body part. post amputation  various cell types contribute to blastema formation  where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps  including DNA methylation and chromatin accessibility  as well as transcriptomes  of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes  coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers  which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map  and a knockout of a predicted upstream regulator disrupts normal regeneration  validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration  and regeneration enhancers are preset as hypomethylated before injury. In contrast  chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing  in duplicate  using Illumina NextSeq.", "parent bioproject:PRJNA523007", "pubmed:32106888", null, "RNA sp7po4dpa rep1", "GSM3611569", null, "tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa", "RNA sp7po4dpa rep1", "Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters:   sjdbScore 1   clip3pAdapterSeq AGATCGGAAGAGC   outWigStrand Unstranded   outFilterType BySJout   outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters:  F GTF  t exon  g gene id  O  s 0   primary  p. Genome build: GRCz10 Supplementary files format and content: TXT", "zebrafish fin", null, "The total RNA was extracted by using TRIzol solution Ambion  according to the manufacturer\u2019s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina  according to the manufacturer\u2019s instructions.", null, "strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa", "GSM3611569", "GSM3611569: RNA sp7po4dpa rep1; Danio rerio; RNA Seq", "GSM3611569", null, "1", "The total RNA was extracted by using TRIzol solution Ambion  according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina  according to the manufacturer's instructions.", "GEO Accession:GSM3611569", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP186180", null, null, "RNA_sp7po4dpa_rep1_R1.fastq.gz RNA_sp7po4dpa_rep1_R2.fastq.gz", "fastq fastq", 8449550100.0, 56330334.0, "GSM3611569 r1", "0:75 1:75", "A:1918679931;C:2308288944;G:2303881576;T:1917610027;N:1089622", 75, 75, null, null, 1918679931, 2308288944, 2303881576, 1917610027, 1089622, "SRX5388267", "SRS4376706", "SRA850124", "GEO", "Ting Wang, Department of Genetics, Washington University School of Medicine", 2, 0.97236, 0.97243, 0.0223, 0.02227, 0.78835, 0.79121, 0.45945, 0.45935, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2019-02-18", "Undetermined", "Undetermined", "Fin", "Surface Structure"]], "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": ["51207"], "units": {}, "query_ms": 9.904414999255096}