{"database": "metadata", "table": "run_metadata", "rows": [[58403, "SRR11305409", "SRX7910549", "SRS6318058", "SRP252754", "PRJNA612515", "Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins", "GSE146960", "Other", "Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.", null, "pubmed:32665240", null, "RNAseq; whole fin; 4dpa; injured; batch 1; rep2", "GSM4411409", null, "source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 4dpa; injured; batch 1; rep2", "RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph", "RNAseq; whole fin; 4dpi; injured", "For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.", "For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month.\u00a0Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank\u2019s Balanced Salt Solution Gibco stirring at 37\u00b0C for 2 hours  collected in 15 minute increments  then strained through a 70 \u03bcm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.", "D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5\u00b0C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.", "time:4 dpa|tissue:whole fin|genotype:wild type", "GSM4411409", "GSM4411409: RNAseq; whole fin; 4dpa; injured; batch 1; rep2; Danio rerio; RNA Seq", "GSM4411409", null, "1", "For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37\u00b0C for 2 hours  collected in 15 minute increments  then strained through a 70 \u03bcm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.", "GEO Accession:GSM4411409", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin.RNAseq_injured_reg2.fastq.gz", "fastq", 2523651950.0, 50473039.0, "GSM4411409 r1", "0:50", "A:658848054;C:605884052;G:596099791;T:662690555;N:129498", 50, null, null, null, 658848054, 605884052, 596099791, 662690555, 129498, "SRX7910549", "SRS6318058", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91959, null, 0.07092, null, 0.70717, null, 0.45829, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-13", "Multi-stage", "Multi-stage", "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": ["58403"], "units": {}, "query_ms": 9.38501900236588}