{"database": "metadata", "table": "run_metadata", "rows": [[30715, "SRR28335986", "SRX23944160", "SRS20746060", "SRP495075", "PRJNA1087403", "CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration RNA Seq", "GSE261539", "Transcriptome Analysis", "The regenerative potential is governed by a complex process of transcriptional reprogramming  involving nuclear reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes influence this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during of zebrafish caudal fin regeneration. Data generated from our protocol recapitulates results from previously published ChIP Seq methods  requires far fewer cells as input  and significantly improves signal to noise ratios during profiling. We deliver high resolution enrichment maps for H3K4me3 at 0 dy post amputation DPA and 2DPA using tissue isolated from caudal fins. During regeneration  we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which are silenced. Remarkably  these epigenetic alterations partially recapitulate H3K4me3 patterns that occur normally in 24 hpf embryos. Our results demonstrate that the CUT&Tag method is an effective tool for profiling chromatin landscapes in regenerating fins  and that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programming. Overall design: RNA sequencing and analysis in 24 hpf zebrafish caudal fin folds", "parent bioproject:PRJNA1087399", "pubmed:38645155;pubmed:39033118", null, "Caudal fin fold  24hpf  rep1", "GSM8146270", null, "source name:fin fold|tissue:fin fold|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing", "Caudal fin fold  24hpf  rep1", "Sequenced reads were trimmed for adaptor sequence  masked for low complexity or low quality sequence  and mapped to danRer11 using STAR aligner Sorted BAM files generated by STAR were processed by deeptools' multibigwigsummary to create RPKM matrix for R's custom scripts to make visualizations bigWig files were also generated using deeptools' bamcoverage with the setting   normalizeUsing RPKM Assembly: danRer11 Supplementary files format and content: bigWig", "fin fold", "caudal fin folds were amputated with 24 hpf embryos", "Fin folds were homogenized immediately post dissection and RNA was extracted using Trizol reagent. . RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:fin fold|genotype:WT|treatment:n1", "GSM8146270", "GSM8146270: Caudal fin fold  24hpf  rep1; Danio rerio; RNA Seq", "GSM8146270 r1", "GSM8146270", "1", "Fin folds were homogenized immediately post dissection and RNA was extracted using Trizol reagent. . RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495075", null, "loader:fastq load.py", "RNAseq_ff_24hpf_rep1_001.fq.gz RNAseq_ff_24hpf_rep1_002.fq.gz", "fastq fastq", 14542846200.0, 48476154.0, "GSM8146270 r1", "0:150 1:150", "A:3861456413;C:3448964037;G:3421753399;T:3810547922;N:124429", 150, 150, null, null, 3861456413, 3448964037, 3421753399, 3810547922, 124429, "SRX23944160", "SRS20746060", "SRA1823686", "University of Rochester", "University of Rochester", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-13", "Pharyngula", "Embryo", "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": ["30715"], "units": {}, "query_ms": 9.148024997557513}