{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and tissue_curation = \"Fin\"", "rows": [[52209, "SRR8992787", "SRX5771765", "SRS4705624", "SRP194294", "PRJNA540521", "Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores", "GSE130526", "Other", "Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates  derived from embryonic neural crest  are a useful system for elucidating mechanisms of fate specification  pattern formation  and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes  including zebrafish Danio rerio  we identified two populations of white pigment cells\u2014leucophores\u2014one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic  mutational  chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions  organelle configurations and genetic requirements. At the organismal level  we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together  our studies revealed new  independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish  and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication", null, "pubmed:31138706", null, "Zebrafish fin pigment cells", "GSM3741778", null, "tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated", "Zebrafish fin pigment cells", "Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.", "Dorsal and anal fins", "Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation  we extracted distal dorsal fin regions 10 mm standard length  SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25\u00b0C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 \u03bcm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 \u03bcg/mL  15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels  single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A  FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence  and then cells from transgenic fish were purified according to these gates. All samples were kept on ice  except during Liberase incubation  and then sorted chilled.", "10X genomics V1 protocol following manufacturer recommendations.", "Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb  a derivative of inbred ABwp  Tgtyrp1b:palm mCherrywp.rt11  Tgpnp4a:palmmCherrywp.rt10", "cell type:pigment cells|treatment:Untreated", "GSM3741778", "GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq", "GSM3741778", null, "1", "10X genomics V1 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP194294", null, null, "leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz", "fastq fastq", 424061944.0, 10241510.0, "GSM3741778 r1", "0:26 1:57", "A:119042142;C:89897538;G:98172861;T:116716009;N:233394", 26, 57, null, null, 119042142, 89897538, 98172861, 116716009, 233394, "SRX5771765", "SRS4705624", "SRA881136", "GEO", "Parichy Lab, Biology, University of Washington", 1, 0.33934, null, 0.07693, null, 0.8742, null, 0.51425, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-04-30", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [58389, "SRR11486781", "SRX8062812", "SRS6431234", "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; LEN deletion; 2dpa; injured; batch 3; rep1", "GSM4455083", null, "source name:whole fin|date:2 dpa|tissue:whole fin", "RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1", "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. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "whole fin", "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.\u00a0Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "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. 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.", "date:2 dpa|tissue:whole fin", "GSM4455083", "GSM4455083: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4455083", 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. 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. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "GEO Accession:GSM4455083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "JK-S8_S75_L008_R1_001.fastq.gz", "fastq", 2464411341.0, 48321791.0, "GSM4455083 r1", "0:51 1:0", "A:620643336;C:590840801;G:549905028;T:702758180;N:263996", 51, 0, null, null, 620643336, 590840801, 549905028, 702758180, 263996, "SRX8062812", "SRS6431234", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91677, null, 0.09917, null, 0.71981, null, 0.46761, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-04-06", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [58390, "SRR11486780", "SRX8062811", "SRS6431233", "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; 2dpa; injured; batch 3; rep1", "GSM4455082", null, "source name:whole fin|date:2 dpa|tissue:whole fin", "RNAseq; whole fin; 2dpa; injured; batch 3; rep1", "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. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "whole fin", "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.\u00a0Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "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. 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.", "date:2 dpa|tissue:whole fin", "GSM4455082", "GSM4455082: RNAseq; whole fin; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4455082", 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. 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. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "GEO Accession:GSM4455082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "JK-S6_S73_L008_R1_001.fastq.gz", "fastq", 2567417214.0, 50341514.0, "GSM4455082 r1", "0:51 1:0", "A:648888081;C:617286062;G:571907197;T:729086777;N:249097", 51, 0, null, null, 648888081, 617286062, 571907197, 729086777, 249097, "SRX8062811", "SRS6431233", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91819, null, 0.10483, null, 0.72062, null, 0.45077, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-04-06", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [58391, "SRR11486779", "SRX8062810", "SRS6431232", "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; LEN deletion; 0dpa; uninjured; batch 3; rep1", "GSM4455081", null, "source name:whole fin|date:0 dpa|tissue:whole fin", "RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1", "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. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "whole fin", "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.\u00a0Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "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. 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.", "date:0 dpa|tissue:whole fin", "GSM4455081", "GSM4455081: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4455081", 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. 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. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "GEO Accession:GSM4455081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "JK-S7_S74_L008_R1_001.fastq.gz", "fastq", 2644840467.0, 51859617.0, "GSM4455081 r1", "0:51 1:0", "A:676588053;C:621109147;G:581574642;T:765307978;N:260647", 51, 0, null, null, 676588053, 621109147, 581574642, 765307978, 260647, "SRX8062810", "SRS6431232", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.89598, null, 0.1281, null, 0.71417, null, 0.47147, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-04-06", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [58392, "SRR11486778", "SRX8062809", "SRS6431231", "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; 0dpa; uninjured; batch 3; rep1", "GSM4455080", null, "source name:whole fin|date:0 dpa|tissue:whole fin", "RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1", "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. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "whole fin", "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.\u00a0Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "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. 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.", "date:0 dpa|tissue:whole fin", "GSM4455080", "GSM4455080: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4455080", 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. 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. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.", "GEO Accession:GSM4455080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "JK-S5_S72_L008_R1_001.fastq.gz", "fastq", 2412481254.0, 47303554.0, "GSM4455080 r1", "0:51 1:0", "A:616219239;C:570826024;G:531833820;T:693353914;N:248257", 51, 0, null, null, 616219239, 570826024, 531833820, 693353914, 248257, "SRX8062809", "SRS6431231", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.90059, null, 0.11572, null, 0.72013, null, 0.46152, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-04-06", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [58393, "SRR11305419", "SRX7910559", "SRS6318068", "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; Fibroblast; 4dpa; injured; batch 3; rep2", "GSM4411419", null, "source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type", "RNAseq; Fibroblast; 4dpa; injured; batch 3; 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; Fibroblast; 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:fibroblast|genotype:wild type", "GSM4411419", "GSM4411419: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2; Danio rerio; RNA Seq", "GSM4411419", 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:GSM4411419", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "Fibro.RNAseq_injured_Regen_B2_S60_L008_R1_001.fastq.gz", "fastq", 3284939427.0, 64410577.0, "GSM4411419 r1", "0:51 1:0", "A:903305689;C:745606629;G:745227959;T:890156683;N:642467", 51, 0, null, null, 903305689, 745606629, 745227959, 890156683, 642467, "SRX7910559", "SRS6318068", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92145, null, 0.11147, null, 0.75091, null, 0.47874, null, 51, 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"], [58394, "SRR11305418", "SRX7910558", "SRS6318067", "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; Fibroblast; 4dpa; injured; batch 3; rep1", "GSM4411418", null, "source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type", "RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1", "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; Fibroblast; 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:fibroblast|genotype:wild type", "GSM4411418", "GSM4411418: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4411418", 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:GSM4411418", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "Fibro.RNAseq_injured_Regen_A2_S59_L008_R1_001.fastq.gz", "fastq", 3208227063.0, 62906413.0, "GSM4411418 r1", "0:51 1:0", "A:889970085;C:720088600;G:719685444;T:877865381;N:617553", 51, 0, null, null, 889970085, 720088600, 719685444, 877865381, 617553, "SRX7910558", "SRS6318067", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91814, null, 0.12108, null, 0.74704, null, 0.51875, null, 51, 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"], [58395, "SRR11305417", "SRX7910557", "SRS6318066", "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; Fibroblast; 0dpa; uninjured; batch 3; rep2", "GSM4411417", null, "source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type", "RNAseq; Fibroblast; 0dpa; uninjured; batch 3; 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; Fibroblast; 0dpi; uninjured", "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:0 dpa|tissue:fibroblast|genotype:wild type", "GSM4411417", "GSM4411417: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2; Danio rerio; RNA Seq", "GSM4411417", 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:GSM4411417", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "Fibro.RNAseq_uninjured_Uninj_B2_S58_L008_R1_001.fastq.gz", "fastq", 3779977251.0, 74117201.0, "GSM4411417 r1", "0:51 1:0", "A:1036587583;C:863955138;G:859693317;T:1019029136;N:712077", 51, 0, null, null, 1036587583, 863955138, 859693317, 1019029136, 712077, "SRX7910557", "SRS6318066", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91762, null, 0.12285, null, 0.7683, null, 0.47877, null, 51, 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"], [58396, "SRR11305416", "SRX7910556", "SRS6318065", "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; Fibroblast; 0dpa; uninjured; batch 3; rep1", "GSM4411416", null, "source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type", "RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1", "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; Fibroblast; 0dpi; uninjured", "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:0 dpa|tissue:fibroblast|genotype:wild type", "GSM4411416", "GSM4411416: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq", "GSM4411416", 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:GSM4411416", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "Fibro.RNAseq_uninjured_Uninj_A2_S57_L008_R1_001.fastq.gz", "fastq", 3830264271.0, 75103221.0, "GSM4411416 r1", "0:51 1:0", "A:1040171853;C:881400891;G:878214685;T:1029746894;N:729948", 51, 0, null, null, 1040171853, 881400891, 878214685, 1029746894, 729948, "SRX7910556", "SRS6318065", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92032, null, 0.09358, null, 0.75771, null, 0.4712, null, 51, 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"], [58397, "SRR11305415", "SRX7910555", "SRS6318064", "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; 1dpa; injured; batch 2; rep3", "GSM4411415", null, "source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 1dpa; injured; batch 2; rep3", "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; 1dpi; 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:1 dpa|tissue:whole fin|genotype:wild type", "GSM4411415", "GSM4411415: RNAseq; whole fin; 1dpa; injured; batch 2; rep3; Danio rerio; RNA Seq", "GSM4411415", 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:GSM4411415", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_injured_RNA_1dpa_A_S37_L004_R1_001.fastq.gz", "fastq", 2924051085.0, 57334335.0, "GSM4411415 r1", "0:51 1:0", "A:678403251;C:734140605;G:692166374;T:819274692;N:66163", 51, 0, null, null, 678403251, 734140605, 692166374, 819274692, 66163, "SRX7910555", "SRS6318064", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93427, null, 0.06589, null, 0.73866, null, 0.45737, null, 51, 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"], [58398, "SRR11305414", "SRX7910554", "SRS6318063", "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; 1dpa; injured; batch 2; rep2", "GSM4411414", null, "source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 1dpa; injured; batch 2; 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; 1dpi; 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:1 dpa|tissue:whole fin|genotype:wild type", "GSM4411414", "GSM4411414: RNAseq; whole fin; 1dpa; injured; batch 2; rep2; Danio rerio; RNA Seq", "GSM4411414", 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:GSM4411414", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_injured_RNA_1dpa_B_S38_L004_R1_001.fastq.gz", "fastq", 3159176895.0, 61944645.0, "GSM4411414 r1", "0:51 1:0", "A:730026525;C:803379127;G:747179794;T:878521357;N:70092", 51, 0, null, null, 730026525, 803379127, 747179794, 878521357, 70092, "SRX7910554", "SRS6318063", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93516, null, 0.07492, null, 0.74602, null, 0.46646, null, 51, 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"], [58399, "SRR11305413", "SRX7910553", "SRS6318062", "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; 1dpa; injured; batch 2; rep1", "GSM4411413", null, "source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 1dpa; injured; batch 2; rep1", "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; 1dpi; 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:1 dpa|tissue:whole fin|genotype:wild type", "GSM4411413", "GSM4411413: RNAseq; whole fin; 1dpa; injured; batch 2; rep1; Danio rerio; RNA Seq", "GSM4411413", 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:GSM4411413", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_injured_RNA_1dpa_C_S39_L004_R1_001.fastq.gz", "fastq", 3053752296.0, 59877496.0, "GSM4411413 r1", "0:51 1:0", "A:705251373;C:775521263;G:724421121;T:848486693;N:71846", 51, 0, null, null, 705251373, 775521263, 724421121, 848486693, 71846, "SRX7910553", "SRS6318062", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.9345, null, 0.08171, null, 0.74326, null, 0.47043, null, 51, 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"], [58400, "SRR11305412", "SRX7910552", "SRS6318061", "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; 0dpa; uninjured; batch 2; rep3", "GSM4411412", null, "source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3", "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; 0dpi; uninjured", "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:0 dpa|tissue:whole fin|genotype:wild type", "GSM4411412", "GSM4411412: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3; Danio rerio; RNA Seq", "GSM4411412", 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:GSM4411412", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_uninjured_RNA_0dpa_B_S35_L004_R1_001.fastq.gz", "fastq", 3095170620.0, 60689620.0, "GSM4411412 r1", "0:51 1:0", "A:728515579;C:769711604;G:717419279;T:879450837;N:73321", 51, 0, null, null, 728515579, 769711604, 717419279, 879450837, 73321, "SRX7910552", "SRS6318061", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91314, null, 0.09911, null, 0.72498, null, 0.46006, null, 51, 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"], [58401, "SRR11305411", "SRX7910551", "SRS6318060", "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; 0dpa; uninjured; batch 2; rep2", "GSM4411411", null, "source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 0dpa; uninjured; batch 2; 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; 0dpi; uninjured", "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:0 dpa|tissue:whole fin|genotype:wild type", "GSM4411411", "GSM4411411: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2; Danio rerio; RNA Seq", "GSM4411411", 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:GSM4411411", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_uninjured_RNA_0dpa_C_S36_L004_R1_001.fastq.gz", "fastq", 2959811163.0, 58035513.0, "GSM4411411 r1", "0:51 1:0", "A:702000960;C:731163416;G:687625038;T:838953116;N:68633", 51, 0, null, null, 702000960, 731163416, 687625038, 838953116, 68633, "SRX7910551", "SRS6318060", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91317, null, 0.09909, null, 0.7237, null, 0.45771, null, 51, 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"], [58402, "SRR11305410", "SRX7910550", "SRS6318059", "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; 0dpa; uninjured; batch 2; rep1", "GSM4411410", null, "source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1", "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; 0dpi; uninjured", "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:0 dpa|tissue:whole fin|genotype:wild type", "GSM4411410", "GSM4411410: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1; Danio rerio; RNA Seq", "GSM4411410", 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:GSM4411410", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin1dpi.RNAseq_uninjured_RNA_0dpa_A_S34_L004_R1_001.fastq.gz", "fastq", 2850762963.0, 55897313.0, "GSM4411410 r1", "0:51 1:0", "A:675289993;C:707558547;G:662291002;T:805558844;N:64577", 51, 0, null, null, 675289993, 707558547, 662291002, 805558844, 64577, "SRX7910550", "SRS6318059", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.91288, null, 0.10801, null, 0.72165, null, 0.46866, null, 51, 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"], [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"], [58404, "SRR11305408", "SRX7910548", "SRS6318057", "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; rep1", "GSM4411408", null, "source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 4dpa; injured; batch 1; rep1", "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", "GSM4411408", "GSM4411408: RNAseq; whole fin; 4dpa; injured; batch 1; rep1; Danio rerio; RNA Seq", "GSM4411408", 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:GSM4411408", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin.RNAseq_injured_reg1.fastq.gz", "fastq", 2490897750.0, 49817955.0, "GSM4411408 r1", "0:50", "A:644634582;C:602186818;G:591877446;T:652072339;N:126565", 50, null, null, null, 644634582, 602186818, 591877446, 652072339, 126565, "SRX7910548", "SRS6318057", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92355, null, 0.06175, null, 0.71342, null, 0.46396, 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"], [58405, "SRR11305407", "SRX7910547", "SRS6318056", "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; 0dpa; uninjured; batch 1; rep2", "GSM4411407", null, "source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 0dpa; uninjured; 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; 0dpi; uninjured", "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:0 dpa|tissue:whole fin|genotype:wild type", "GSM4411407", "GSM4411407: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2; Danio rerio; RNA Seq", "GSM4411407", 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:GSM4411407", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin.RNAseq_uninjured_Uni2.fastq.gz", "fastq", 1646067800.0, 32921356.0, "GSM4411407 r1", "0:50", "A:433931789;C:391550599;G:380315477;T:440186224;N:83711", 50, null, null, null, 433931789, 391550599, 380315477, 440186224, 83711, "SRX7910547", "SRS6318056", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.90771, null, 0.08897, null, 0.71985, null, 0.44509, 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"], [58406, "SRR11305406", "SRX7910546", "SRS6318055", "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; 0dpa; uninjured; batch 1; rep1", "GSM4411406", null, "source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type", "RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1", "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; 0dpi; uninjured", "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:0 dpa|tissue:whole fin|genotype:wild type", "GSM4411406", "GSM4411406: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1; Danio rerio; RNA Seq", "GSM4411406", 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:GSM4411406", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP252754", null, null, "WFin.RNAseq_uninjured_Uni1.fastq.gz", "fastq", 2093137350.0, 41862747.0, "GSM4411406 r1", "0:50", "A:539953107;C:505949113;G:500993563;T:546137713;N:103854", 50, null, null, null, 539953107, 505949113, 500993563, 546137713, 103854, "SRX7910546", "SRS6318055", "SRA1054723", "GEO", "Poss, Cell Biology, Duke University", 1, 0.9119, null, 0.07318, null, 0.72969, null, 0.43282, 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"]], "truncated": false, "filtered_table_rows_count": 19, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Multi-stage", "p1": "Fin"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Fin", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Fin&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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