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409 rows where devstage_curation_coarse = "Adult" and tissue_curation = "Fin"

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technology 7

experiment.library_selection 7

experiment.platform 5

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Fin · 409 ✖

devstage_curation_coarse 1

  • Adult · 409 ✖
Link 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
282 282 DRR179616 DRX170142 DRS185505 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin xanthophore 03 SAMD00172019   sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172019 DRX170142 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172019       376558775.0 1624500.0 DRR179616 0:231.80 A:107837072;C:79508449;G:79372899;T:109840355;N:0 231       107837072 79508449 79372899 109840355 0 DRX170142 DRS185505 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.86944   0.10951   0.90425   0.59385   311   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
283 283 DRR179615 DRX170141 DRS185504 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 02 SAMD00172018   sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172018 DRX170141 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172018       515115515.0 2124170.0 DRR179615 0:242.50 A:138421982;C:119032803;G:119412227;T:138248503;N:0 242       138421982 119032803 119412227 138248503 0 DRX170141 DRS185504 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88998   0.05858   0.88051   0.50917   284   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
284 284 DRR179614 DRX170140 DRS185503 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 01 SAMD00172017   sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172017 DRX170140 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172017       371242152.0 1504407.0 DRR179614 0:246.77 A:99341086;C:86126839;G:86264882;T:99509345;N:0 246       99341086 86126839 86264882 99509345 0 DRX170140 DRS185503 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88672   0.06422   0.85679   0.5066   56   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
285 285 DRR179613 DRX170139 DRS185502 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin melanophore 03 SAMD00172016   sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172016 DRX170139 Zebrafish fin melanophore 03 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172016       342802993.0 1585538.0 DRR179613 0:216.21 A:90833658;C:80789744;G:80463233;T:90716358;N:0 216       90833658 80789744 80463233 90716358 0 DRX170139 DRS185502 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.8312   0.03528   0.88605   0.47299   285   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
286 286 DRR179612 DRX170138 DRS185501 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 02 SAMD00172015   sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172015 DRX170138 Zebrafish fin melanophore 02 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172015       538412675.0 2168231.0 DRR179612 0:248.32 A:147128403;C:121854818;G:121564109;T:147865345;N:0 248       147128403 121854818 121564109 147865345 0 DRX170138 DRS185501 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.89106   0.07081   0.89286   0.5935   283   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
287 287 DRR179611 DRX170137 DRS185500 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 01 SAMD00172014   sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172014 DRX170137 Zebrafish fin melanophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172014       282446840.0 1311431.0 DRR179611 0:215.37 A:74927237;C:66575483;G:66161471;T:74782649;N:0 215       74927237 66575483 66161471 74782649 0 DRX170137 DRS185500 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.85938   0.0335   0.89248   0.58813   274   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
288 288 DRR224554 DRX214839 DRS236362 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish Adult C SAMD00222585   sample name:Adult C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222585 DRX214839 Adult C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222585       11727505800.0 58637529.0 DRR224554 0:100 1:100 A:3137648588;C:2705013210;G:3191753451;T:2692963496;N:127055 100 100     3137648588 2705013210 3191753451 2692963496 127055 DRX214839 DRS236362 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.95934 0.93156 0.03853 0.0394 0.72683 0.74625 0.45812 0.47098 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Adult Adult Fin Surface Structure
289 289 DRR224553 DRX214838 DRS236361 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish Adult B SAMD00222584   sample name:Adult B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222584 DRX214838 Adult B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222584       22010855600.0 110054278.0 DRR224553 0:100 1:100 A:5511440112;C:5498539659;G:5546758172;T:5453879750;N:237907 100 100     5511440112 5498539659 5546758172 5453879750 237907 DRX214838 DRS236361 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.95774 0.95394 0.04568 0.04411 0.70701 0.70881 0.47041 0.47938 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Adult Adult Fin Surface Structure
290 290 DRR224552 DRX214837 DRS236360 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish Adult A SAMD00222583   sample name:Adult A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222583 DRX214837 Adult A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222583       17683281000.0 88416405.0 DRR224552 0:100 1:100 A:4386756926;C:4479415938;G:4578796094;T:4238125580;N:186462 100 100     4386756926 4479415938 4578796094 4238125580 186462 DRX214837 DRS236360 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.95974 0.95566 0.05237 0.05086 0.74357 0.74742 0.48578 0.49971 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Adult Adult Fin Surface Structure
29191 29191 SRR27308233 SRX22985581 SRS19950789 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP /sp7+ Osteoblast rep2 GSM7987448   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP /sp7+ Osteoblast rep2 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987448 GSM7987448: EGFP /sp7+ Osteoblast rep2; Danio rerio; RNA Seq GSM7987448 r1 GSM7987448 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Ob-GR2_S6_R2_001.fastq.gz Ob-GR2_S6_R1_001.fastq.gz fastq fastq 6044999600.0 15112499.0 GSM7987448 r1 0:200 1:200 A:1547731745;C:1388120378;G:1581574912;T:1523597213;N:3975352 200 200     1547731745 1388120378 1581574912 1523597213 3975352 SRX22985581 SRS19950789 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.36888 0.02272 0.01109 0.00038 0.86914 0.99328 0.46943 0.4982 200 200 B T mate2 technical by mapping diff bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
29192 29192 SRR27308234 SRX22985580 SRS19950790 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP /sp7+ Osteoblast rep1 GSM7987447   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP /sp7+ Osteoblast rep1 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987447 GSM7987447: EGFP /sp7+ Osteoblast rep1; Danio rerio; RNA Seq GSM7987447 r1 GSM7987447 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Ob-GR_S77_R1_001.fastq.gz Ob-GR_S77_R2_001.fastq.gz fastq fastq 4847773600.0 12119434.0 GSM7987447 r1 0:200 1:200 A:1242312480;C:1120397684;G:1256425065;T:1226991694;N:1646677 200 200     1242312480 1120397684 1256425065 1226991694 1646677 SRX22985580 SRS19950790 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.0146 0.02559 0.00038 0.00052 0.99397 0.99405 0.50471 0.47146 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
29193 29193 SRR27308235 SRX22985579 SRS19950788 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP+/sp7+ OMP rep2 GSM7987446   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP+/sp7+ OMP rep2 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987446 GSM7987446: EGFP+/sp7+ OMP rep2; Danio rerio; RNA Seq GSM7987446 r1 GSM7987446 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Ob-G2_S5_R2_001.fastq.gz Ob-G2_S5_R1_001.fastq.gz fastq fastq 6253558800.0 15633897.0 GSM7987446 r1 0:200 1:200 A:1638931864;C:1404420075;G:1600115132;T:1605939571;N:4152158 200 200     1638931864 1404420075 1600115132 1605939571 4152158 SRX22985579 SRS19950788 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.41021 0.02334 0.01523 0.00074 0.83989 0.99099 0.52255 0.52173 200 200 B T mate2 technical by mapping diff bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
29194 29194 SRR27308236 SRX22985578 SRS19950791 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP+/sp7+ OMP rep1 GSM7987445   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP+/sp7+ OMP rep1 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987445 GSM7987445: EGFP+/sp7+ OMP rep1; Danio rerio; RNA Seq GSM7987445 r1 GSM7987445 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Ob-G_S28_R2_001.fastq.gz Ob-G_S28_R1_001.fastq.gz fastq fastq 4832320400.0 12080801.0 GSM7987445 r1 0:200 1:200 A:1252095509;C:1107971153;G:1236349772;T:1233319775;N:2584191 200 200     1252095509 1107971153 1236349772 1233319775 2584191 SRX22985578 SRS19950791 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01133 0.02895 0.00033 0.00043 0.99439 0.99297 0.50298 0.45574 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
29195 29195 SRR27308237 SRX22985577 SRS19950787 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP+/sp7 CMP rep2 GSM7987444   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP+/sp7 CMP rep2 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987444 GSM7987444: EGFP+/sp7 CMP rep2; Danio rerio; RNA Seq GSM7987444 r1 GSM7987444 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Mes-G2_S4_R1_001.fastq.gz Mes-G2_S4_R2_001.fastq.gz fastq fastq 5812163600.0 14530409.0 GSM7987444 r1 0:200 1:200 A:1538664561;C:1291748975;G:1473028809;T:1504905134;N:3816121 200 200     1538664561 1291748975 1473028809 1504905134 3816121 SRX22985577 SRS19950787 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.40138 0.02482 0.0176 0.00091 0.83918 0.99099 0.47875 0.43124 200 200 B T mate2 technical by mapping diff bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
29196 29196 SRR27308238 SRX22985576 SRS19950786 SRP479308 PRJNA1055256 Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish GSE251757 Transcriptome Analysis Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.   pubmed:38193362   EGFP+/sp7 CMP rep1 GSM7987443   source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing EGFP+/sp7 CMP rep1 High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values. 14 dpa adult caudal fin Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry GSM7987443 GSM7987443: EGFP+/sp7 CMP rep1; Danio rerio; RNA Seq GSM7987443 r1 GSM7987443 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP479308     Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz fastq fastq 5321588000.0 13303970.0 GSM7987443 r1 0:200 1:200 A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516 200 200     1405233304 1195662643 1342003810 1376732727 1955516 SRX22985576 SRS19950786 SRA1773396 Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.00961 0.02419 0.00032 0.00052 0.9945 0.99324 0.51073 0.48429 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-12-20 Adult Adult Fin Surface Structure
30628 30628 SRR27942672 SRX23599456 SRS20442304 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   6 day post amputation replicate 2 6dpa fin2   strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 2|BioSampleModel:Model organism or animal                 6dpa fin2 snRNA 6dpa2 RNA 6dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     6dpa2-GEX-lib1_S2_L001_R2_001.fastq.gz 6dpa2-GEX-lib1_S2_L001_R1_001.fastq.gz fastq fastq 88818703262.0 498981479.0 6dpa2 GEX lib1 S2 L001 R1 001.fastq.gz 0:28 1:150 A:27051219358;C:18185699713;G:19496959258;T:24083822607;N:1002326 28 150     27051219358 18185699713 19496959258 24083822607 1002326 SRX23599456 SRS20442304 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02864 0.84751 0.01449 0.29092 0.98169 0.82014 0.39586 0.64356 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30629 30629 SRR27942673 SRX23599455 SRS20442303 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   6 day post amputation replicate 1 6dpa fin1   strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 1|BioSampleModel:Model organism or animal                 6dpa fin1 snRNA 6dpa1 RNA 6dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     6dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 6dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz fastq fastq 106483322870.0 598220915.0 6dpa1 GEX lib1 S1 L001 R1 001.fastq.gz 0:28 1:150 A:32833929738;C:22259209515;G:23233729505;T:28155235335;N:1218777 28 150     32833929738 22259209515 23233729505 28155235335 1218777 SRX23599455 SRS20442303 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02691 0.87324 0.01263 0.22013 0.98415 0.83144 0.4808 0.62463 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30630 30630 SRR27942674 SRX23599454 SRS20442302 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   4 day post amputation replicate 2 4dpa fin2   strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 2|BioSampleModel:Model organism or animal                 4dpa fin2 snRNA 4dpa2 RNA 4dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     4dpa2-GEX-lib1_S2_L002_R1_001.fastq.gz 4dpa2-GEX-lib1_S2_L002_R2_001.fastq.gz fastq fastq 100355045420.0 563792390.0 4dpa2 GEX lib1 S2 L002 R1 001.fastq.gz 0:28 1:150 A:30110360316;C:21497825420;G:22061747902;T:26684746811;N:364971 28 150     30110360316 21497825420 22061747902 26684746811 364971 SRX23599454 SRS20442302 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02956 0.90492 0.01391 0.21143 0.98324 0.82347 0.46993 0.73177 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30631 30631 SRR27942675 SRX23599453 SRS20442301 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   4 day post amputation replicate 1 4dpa fin1   strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 1|BioSampleModel:Model organism or animal                 4dpa fin1 snRNA 4dpa1 RNA 4dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     4dpa1-GEX-lib1_S1_L002_R2_001.fastq.gz 4dpa1-GEX-lib1_S1_L002_R1_001.fastq.gz fastq fastq 104945766346.0 589582957.0 4dpa1 GEX lib1 S1 L002 R1 001.fastq.gz 0:28 1:150 A:32489394291;C:21756067815;G:22868928766;T:27829952922;N:1422552 28 150     32489394291 21756067815 22868928766 27829952922 1422552 SRX23599453 SRS20442301 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02921 0.86985 0.01399 0.22211 0.98372 0.8294 0.45783 0.71655 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30632 30632 SRR27942676 SRX23599452 SRS20442300 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   2 day post amputation replicate 2 2dpa fin2   strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 2|BioSampleModel:Model organism or animal                 2dpa fin2 snRNA 2dpa2 RNA 2dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     2dpa2-GEX-lib1_S1_L001_R2_001.fastq.gz 2dpa2-GEX-lib1_S1_L001_R1_001.fastq.gz fastq fastq 84977307334.0 477400603.0 2dpa2 GEX lib1 S1 L001 R1 001.fastq.gz 0:28 1:150 A:25498895454;C:18439149160;G:19015549944;T:22023275686;N:437090 28 150     25498895454 18439149160 19015549944 22023275686 437090 SRX23599452 SRS20442300 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02811 0.91493 0.01297 0.18571 0.98492 0.83554 0.4671 0.75085 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30633 30633 SRR27942677 SRX23599451 SRS20442299 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   2 day post amputation replicate 1 2dpa fin1   strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 1|BioSampleModel:Model organism or animal                 2dpa fin1 snRNA 2dpa1 RNA 2dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     2dpa1-GEX-lib1_S2_L002_R1_001.fastq.gz 2dpa1-GEX-lib1_S2_L002_R2_001.fastq.gz fastq fastq 93046027220.0 522730490.0 2dpa1 GEX lib1 S2 L002 R1 001.fastq.gz 0:28 1:150 A:28562453325;C:19484276400;G:20294346104;T:24703683984;N:1267407 28 150     28562453325 19484276400 20294346104 24703683984 1267407 SRX23599451 SRS20442299 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.03074 0.88234 0.01398 0.22441 0.98405 0.83268 0.48065 0.74026 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30634 30634 SRR27942678 SRX23599450 SRS20442298 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   1 day post amputation replicate 2 1dpa fin2   strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 2|BioSampleModel:Model organism or animal                 1dpa fin2 snRNA 1dpa2 RNA 1dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     1dpa2-GEX-lib1_S1_L004_R1_001.fastq.gz 1dpa2-GEX-lib1_S1_L004_R2_001.fastq.gz fastq fastq 84562055050.0 475067725.0 1dpa2 GEX lib1 S1 L004 R1 001.fastq.gz 0:28 1:150 A:25830017026;C:17874013165;G:18722117096;T:22135719607;N:188156 28 150     25830017026 17874013165 18722117096 22135719607 188156 SRX23599450 SRS20442298 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02723 0.88745 0.01218 0.18561 0.98573 0.83613 0.45958 0.63016 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30635 30635 SRR27942679 SRX23599449 SRS20442297 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   1 day post amputation replicate 1 1dpa fin1   strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 1|BioSampleModel:Model organism or animal                 1dpa fin1 snRNA 1dpa1 RNA 1dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     1dpa1-GEX-lib1_S3_L002_R2_002.fastq.gz 1dpa1-GEX-lib1_S3_L002_R1_002.fastq.gz 1dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 1dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz fastq fastq fastq fastq 81494415866.0 457833797.0 1dpa1 GEX lib1 S1 L001 R1 001.fastq.gz 0:28 1:150 A:25109914971;C:16807439152;G:17406389176;T:22169842983;N:829584 28 150     25109914971 16807439152 17406389176 22169842983 829584 SRX23599449 SRS20442297 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02792 0.87908 0.0123 0.19441 0.98194 0.83644 0.4621 0.70445 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30636 30636 SRR27942690 SRX23599438 SRS20442296 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   0 day post amputation replicate 2 0dpa fin2   strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 2|BioSampleModel:Model organism or animal                 0dpa fin2 snRNA 0dpa2 RNA 0dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     0dpa2-GEX-lib1_S2_L004_R2_001.fastq.gz 0dpa2-GEX-lib1_S2_L004_R1_001.fastq.gz fastq fastq 94016384252.0 528181934.0 0dpa2 GEX lib1 S2 L004 R1 001.fastq.gz 0:28 1:150 A:28851000041;C:19680536935;G:20640186670;T:24844451695;N:208911 28 150     28851000041 19680536935 20640186670 24844451695 208911 SRX23599438 SRS20442296 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02684 0.87686 0.01274 0.21544 0.98703 0.85975 0.45722 0.74164 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
30637 30637 SRR27942691 SRX23599437 SRS20442295 SRP489317 PRJNA1075480 Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution PRJNA1075480 Other Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1 2 4 and 6 dy post amputation dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.   pubmed:39809530   0 day post amputation replicate 1 0dpa fin1   strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 1|BioSampleModel:Model organism or animal                 0dpa fin1 snRNA 0dpa1 RNA 0dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     0dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz 0dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz fastq fastq 95106992388.0 534308946.0 0dpa1 GEX lib1 S1 L001 R1 001.fastq.gz 0:28 1:150 A:29570202174;C:19531427210;G:20167731244;T:25836092390;N:1539370 28 150     29570202174 19531427210 20167731244 25836092390 1539370 SRX23599437 SRS20442295 SRA1801018 Washington University in St. Louis School of Medicine|Genetics Washington University in St. Louis School of Medicine 2 0.02388 0.87039 0.01162 0.24031 0.98652 0.85354 0.48963 0.74378 28 150 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-02-12 Adult Adult Fin Surface Structure
35557 35557 SRR32880273 SRX28160884 SRS24513822 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 5 GSM8875053   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 5 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875053 GSM8875053: 3dpa blastema exercised exp bio rep 5; Danio rerio; RNA Seq GSM8875053 r1 GSM8875053 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_5_raw.fastq.gz fastq 3833406286.0 31421363.0 GSM8875053 r1 0:122 A:1051289152;C:808410920;G:908646262;T:1064964960;N:94992 122       1051289152 808410920 908646262 1064964960 94992 SRX28160884 SRS24513822 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35558 35558 SRR32880274 SRX28160883 SRS24513821 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 4 GSM8875052   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 4 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875052 GSM8875052: 3dpa blastema exercised exp bio rep 4; Danio rerio; RNA Seq GSM8875052 r1 GSM8875052 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_4_raw.fastq.gz fastq 2716320484.0 22264922.0 GSM8875052 r1 0:122 A:753716648;C:572683669;G:633777091;T:756074187;N:68889 122       753716648 572683669 633777091 756074187 68889 SRX28160883 SRS24513821 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35559 35559 SRR32880275 SRX28160882 SRS24513820 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 3 GSM8875051   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 3 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875051 GSM8875051: 3dpa blastema exercised exp bio rep 3; Danio rerio; RNA Seq GSM8875051 r1 GSM8875051 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_3_raw.fastq.gz fastq 3326494944.0 27266352.0 GSM8875051 r1 0:122 A:929692130;C:705713811;G:773972336;T:917030832;N:85835 122       929692130 705713811 773972336 917030832 85835 SRX28160882 SRS24513820 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35560 35560 SRR32880276 SRX28160881 SRS24513819 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 2 GSM8875050   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 2 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875050 GSM8875050: 3dpa blastema exercised exp bio rep 2; Danio rerio; RNA Seq GSM8875050 r1 GSM8875050 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_2_raw.fastq.gz fastq 3319809954.0 27211557.0 GSM8875050 r1 0:122 A:912008882;C:704589377;G:783108238;T:920018852;N:84605 122       912008882 704589377 783108238 920018852 84605 SRX28160881 SRS24513819 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35561 35561 SRR32880277 SRX28160880 SRS24513818 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema exercised exp bio rep 1 GSM8875049   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing 3dpa blastema exercised exp bio rep 1 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised GSM8875049 GSM8875049: 3dpa blastema exercised exp bio rep 1; Danio rerio; RNA Seq GSM8875049 r1 GSM8875049 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Exp_1_raw.fastq.gz fastq 3744436322.0 30692101.0 GSM8875049 r1 0:122 A:1050863937;C:775277972;G:866627322;T:1051571183;N:95908 122       1050863937 775277972 866627322 1051571183 95908 SRX28160880 SRS24513818 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35562 35562 SRR32880278 SRX28160879 SRS24513817 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 5 GSM8875048   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 5 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875048 GSM8875048: 3dpa blastema unexercised control bio rep 5; Danio rerio; RNA Seq GSM8875048 r1 GSM8875048 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_5_raw.fastq.gz fastq 3076092628.0 25213874.0 GSM8875048 r1 0:122 A:850913805;C:643783202;G:725071885;T:856245838;N:77898 122       850913805 643783202 725071885 856245838 77898 SRX28160879 SRS24513817 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35563 35563 SRR32880279 SRX28160878 SRS24513816 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 4 GSM8875047   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 4 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875047 GSM8875047: 3dpa blastema unexercised control bio rep 4; Danio rerio; RNA Seq GSM8875047 r1 GSM8875047 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_4_raw.fastq.gz fastq 3458014848.0 28344384.0 GSM8875047 r1 0:122 A:946385067;C:748704825;G:821787294;T:941050744;N:86918 122       946385067 748704825 821787294 941050744 86918 SRX28160878 SRS24513816 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35564 35564 SRR32880280 SRX28160877 SRS24513815 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 3 GSM8875046   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 3 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875046 GSM8875046: 3dpa blastema unexercised control bio rep 3; Danio rerio; RNA Seq GSM8875046 r1 GSM8875046 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_3_raw.fastq.gz fastq 3750141896.0 30738868.0 GSM8875046 r1 0:122 A:1016915650;C:830734179;G:908080650;T:994316527;N:94890 122       1016915650 830734179 908080650 994316527 94890 SRX28160877 SRS24513815 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35565 35565 SRR32880281 SRX28160876 SRS24513814 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 2 GSM8875045   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 2 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875045 GSM8875045: 3dpa blastema unexercised control bio rep 2; Danio rerio; RNA Seq GSM8875045 r1 GSM8875045 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_2_raw.fastq.gz fastq 3559797740.0 29178670.0 GSM8875045 r1 0:122 A:940502236;C:815297194;G:877321806;T:926584991;N:91513 122       940502236 815297194 877321806 926584991 91513 SRX28160876 SRS24513814 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
35566 35566 SRR32880282 SRX28160875 SRS24513812 SRP573530 PRJNA1242724 Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration GSE293062 Transcriptome Analysis Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading initiated before or during blastema formation resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program including for hyaluronic acid HA synthesis. Like exercise loading HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair where early exercise—applied during blastema establishment—impairs regeneration while delayed loading during outgrowth does not suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control       3dpa blastema unexercised control bio rep 1 GSM8875044   source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing 3dpa blastema unexercised control bio rep 1 Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files whole caudal fin 3 dpa blastema Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later. RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library. Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control GSM8875044 GSM8875044: 3dpa blastema unexercised control bio rep 1; Danio rerio; RNA Seq GSM8875044 r1 GSM8875044 1 RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit indexed and pooled and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP573530     Control_1_raw.fastq.gz fastq 3410581248.0 27955584.0 GSM8875044 r1 0:122 A:908666390;C:784237057;G:832115119;T:885476069;N:86613 122       908666390 784237057 832115119 885476069 86613 SRX28160875 SRS24513812 SRA2100952 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2025-03-27 Adult Adult Fin Surface Structure
36617 36617 SRR941753 SRX326770 SRS463196 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 2 Pos2   strain:EK|isolate:4|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 2 Pectoral Posterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Pos_R2.fastq fastq 2119489050.0 42389781.0 Pos R2 0:50 A:551122430;C:507870866;G:499494183;T:555469321;N:5532250 50       551122430 507870866 499494183 555469321 5532250 SRX326770 SRS463196 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.90238   0.08924   0.71303   0.43405   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36618 36618 SRR941754 SRX326769 SRS463195 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 1 Pos1   strain:EK|isolate:3|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 1 Pectoral Fin Posterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598         1839141950.0 36782839.0 Pos R1 0:50 A:461313296;C:455413049;G:451484067;T:466101993;N:4829545 50       461313296 455413049 451484067 466101993 4829545 SRX326769 SRS463195 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.91205   0.06923   0.71656   0.42651   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36619 36619 SRR941751 SRX326756 SRS463187 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 2 Ant2   strain:EK|isolate:2|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 2 Pectoral Fin Anterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R2.fastq fastq 2146396250.0 42927925.0 Ant R2 0:50 A:562140204;C:509390346;G:501995610;T:567232459;N:5637631 50       562140204 509390346 501995610 567232459 5637631 SRX326756 SRS463187 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89956   0.09279   0.70997   0.44847   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36620 36620 SRR941749 SRX326754 SRS463185 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 1 Ant1   strain:EK|isolate:1|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 1 Pectoral Fin Anterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R1.fastq fastq 2178096950.0 43561939.0 Ant R1 0:50 A:568580441;C:517705965;G:509551928;T:576519788;N:5738828 50       568580441 517705965 509551928 576519788 5738828 SRX326754 SRS463185 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89833   0.08959   0.71494   0.44088   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
38032 38032 SRR1299129 SRX553173 SRS620472 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     Seven days time post treatment   7DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:7 days time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 6 1 TruSeq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     7DZF-Danio_rerio_1R.fastq.bz2 7DZF-Danio_rerio_2R.fastq.bz2 fastq fastq 6699100124.0 33163862.0 7DZF 0:101 1:101 A:1884401354;C:1480292513;G:1459626078;T:1874377806;N:402373 101 101     1884401354 1480292513 1459626078 1874377806 402373 SRX553173 SRS620472 SRA166158 CCMB|CCMB CCMB 2 0.92782 0.93012 0.08953 0.09016 0.72512 0.72693 0.50289 0.50368 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2015-05-01 Adult Adult Fin Surface Structure
38033 38033 SRR1299128 SRX553172 SRS620471 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     Three days time post treatment   3DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:3e days time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 5 1 TruSeq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     3DZF-Danio_rerio_1R.fastq.bz2 3DZF-Danio_rerio_2R.fastq.bz2 fastq fastq 6020171862.0 29802831.0 3DZF 0:101 1:101 A:1658934475;C:1364088259;G:1346830828;T:1649957848;N:360452 101 101     1658934475 1364088259 1346830828 1649957848 360452 SRX553172 SRS620471 SRA166158 CCMB|CCMB CCMB 2 0.93196 0.93157 0.09004 0.09098 0.71906 0.72157 0.48732 0.4861 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2014-05-27 Adult Adult Fin Surface Structure
38034 38034 SRR1299127 SRX553171 SRS620470 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     Two days time post treatment   2DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:2 days time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 4 1 TruSeq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     2DZF-Danio_rerio_1R.fastq.bz2 2DZF-Danio_rerio_2R.fastq.bz2 fastq fastq 6925437084.0 34284342.0 2DZF 0:101 1:101 A:1948705184;C:1527739911;G:1509464867;T:1939201870;N:325252 101 101     1948705184 1527739911 1509464867 1939201870 325252 SRX553171 SRS620470 SRA166158 CCMB|CCMB CCMB 2 0.92094 0.9222 0.08397 0.08467 0.73322 0.73499 0.49436 0.4896 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2015-05-01 Adult Adult Fin Surface Structure
38035 38035 SRR1299126 SRX553170 SRS620469 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     One day time post treatment   1DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:1 day time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 3 1 TruSeq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     1DZF-Danio_rerio_2R.fastq.bz2 1DZF-Danio_rerio_1R.fastq.bz2 fastq fastq 6719993388.0 33267294.0 1DZF 0:101 1:101 A:1893609768;C:1482166949;G:1462366567;T:1881531262;N:318842 101 101     1893609768 1482166949 1462366567 1881531262 318842 SRX553170 SRS620469 SRA166158 CCMB|CCMB CCMB 2 0.92967 0.93015 0.08097 0.08125 0.74213 0.74324 0.47392 0.48207 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2014-05-27 Adult Adult Fin Surface Structure
38036 38036 SRR1299125 SRX553169 SRS620468 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     Half day time post treatment   1 2DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:Half day time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 2 1 TruSeq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     1-2DZF-Danio_rerio_2R.fastq.bz2 1-2DZF-Danio_rerio_1R.fastq.bz2 fastq fastq 6236131678.0 30871939.0 1 2DZF 0:101 1:101 A:1762641472;C:1370283862;G:1350562716;T:1752265045;N:378583 101 101     1762641472 1370283862 1350562716 1752265045 378583 SRX553169 SRS620468 SRA166158 CCMB|CCMB CCMB 2 0.92407 0.92539 0.08396 0.08553 0.74456 0.74716 0.50446 0.51234 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2014-05-27 Adult Adult Fin Surface Structure
38037 38037 SRR1299124 SRX553168 SRS620467 SRP042111 PRJNA248169 Danio rerio strain:Wild Transcriptome or Gene expression PRJNA248169 Other Differential transcriptome map of Zebrafish Caudal fin     Zero day time post treatment   0DZF   breed:Wild|strain:Wild|age:1 Year|biomaterial provider:Caudal fin tissue|sex:not applicable|tissue:Caudal fin|time point:Zero day time point|BioSampleModel:Model organism or animal                 Danio rerio Transcriptome or Gene expression Danio rerioPRJNA248169 1 Truseq adapter were used.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP042111     0DZF-Danio_rerio_1R.fastq.bz2 0DZF-Danio_rerio_2R.fastq.bz2 fastq fastq 6698814092.0 33162446.0 0DZF 0:101 1:101 A:1835032668;C:1528628655;G:1505878886;T:1828956105;N:317778 101 101     1835032668 1528628655 1505878886 1828956105 317778 SRX553168 SRS620467 SRA166158 CCMB|CCMB CCMB 2 0.92038 0.92069 0.08892 0.08995 0.74511 0.74686 0.44111 0.43423 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   India 2015-05-01 Adult Adult Fin Surface Structure
39609 39609 SRR1873571 SRX915251 SRS870223 SRP056014 PRJNA277780 Identification of small non coding RNAs in zebrafish GSE66718 Transcriptome Analysis MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.   pubmed:26694924   fins GSM1630515   source name:adult fins 1 year old|strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year fins Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs… adult fins 1 year old   100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle. strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year GSM1630515 GSM1630515: fins; Danio rerio; miRNA Seq GSM1630515   1 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. GEO Accession:GSM1630515 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE LS454 454 GS FLX   SRP056014         113161.0 2108.0 GSM1630515 r1 0:4 1:49.68 A:30303;C:30710;G:27210;T:24785;N:153 4 49     30303 30710 27210 24785 153 SRX915251 SRS870223 SRA246117 GEO University of Aveiro 1 0.0   0.0   1.0       50   T   under 1.2% mapping rate legacy early 3prime size_fractionation unknown bulk other_seq 454   Portugal 2015-03-09 Adult Adult Fin Surface Structure
40086 40086 SRR2834979 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s1_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 630601950.0 4204013.0 GSM1920166 r1 0:75 1:75 A:171271145;C:143912091;G:143285443;T:171898196;N:235075 75 75     171271145 143912091 143285443 171898196 235075 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93406 0.93511 0.09798 0.09749 0.72849 0.72837 0.47711 0.45945 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40087 40087 SRR2834980 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s2_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 628267350.0 4188449.0 GSM1920166 r2 0:75 1:75 A:170714188;C:143336684;G:142647276;T:171364590;N:204612 75 75     170714188 143336684 142647276 171364590 204612 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93453 0.9359 0.09777 0.0975 0.72616 0.72579 0.47268 0.4644 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40088 40088 SRR2834981 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s3_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 626516250.0 4176775.0 GSM1920166 r3 0:75 1:75 A:170187394;C:142926866;G:142268364;T:170794170;N:339456 75 75     170187394 142926866 142268364 170794170 339456 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93446 0.93568 0.09848 0.09862 0.72784 0.72585 0.47802 0.47051 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40089 40089 SRR2834982 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s4_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 627436050.0 4182907.0 GSM1920166 r4 0:75 1:75 A:170423053;C:143133290;G:142420344;T:171065934;N:393429 75 75     170423053 143133290 142420344 171065934 393429 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93424 0.93534 0.09888 0.09874 0.72959 0.72723 0.47804 0.46597 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40090 40090 SRR2834983 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s5_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 629291250.0 4195275.0 GSM1920166 r5 0:75 1:75 A:170972063;C:143614492;G:142878509;T:171605906;N:220280 75 75     170972063 143614492 142878509 171605906 220280 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93519 0.93675 0.09682 0.09705 0.72859 0.72734 0.47355 0.46593 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40091 40091 SRR2834984 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s6_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 627426000.0 4182840.0 GSM1920166 r6 0:75 1:75 A:170488454;C:143217206;G:142475719;T:171106265;N:138356 75 75     170488454 143217206 142475719 171106265 138356 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93423 0.93616 0.09693 0.0976 0.7263 0.72506 0.46667 0.44848 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40092 40092 SRR2834985 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s7_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 631210500.0 4208070.0 GSM1920166 r7 0:75 1:75 A:171480869;C:144041570;G:143298205;T:172164864;N:224992 75 75     171480869 144041570 143298205 172164864 224992 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93391 0.93472 0.09737 0.09776 0.72801 0.72622 0.47605 0.47398 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40093 40093 SRR2834986 SRX1389538 SRS1136855 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 3 GSM1920166   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920166 GSM1920166: 4dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920166   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920166 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_24_SL87437.fastq.gz C6E48ANXX_s8_2_GSLv3-7_24_SL87437.fastq.gz fastq fastq 633219450.0 4221463.0 GSM1920166 r8 0:75 1:75 A:172056421;C:144444633;G:143727097;T:172865744;N:125555 75 75     172056421 144444633 143727097 172865744 125555 SRX1389538 SRS1136855 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93455 0.9344 0.09681 0.09591 0.7277 0.72667 0.47137 0.47086 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40094 40094 SRR2834971 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s1_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 489505650.0 3263371.0 GSM1920165 r1 0:75 1:75 A:133758989;C:110888626;G:110559204;T:134105559;N:193272 75 75     133758989 110888626 110559204 134105559 193272 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92817 0.92927 0.10941 0.10814 0.72123 0.72314 0.47381 0.47471 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40095 40095 SRR2834972 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s2_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 488869350.0 3259129.0 GSM1920165 r2 0:75 1:75 A:133645391;C:110722394;G:110362752;T:133964152;N:174661 75 75     133645391 110722394 110362752 133964152 174661 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92828 0.93043 0.10881 0.10857 0.72139 0.72411 0.49072 0.48574 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40096 40096 SRR2834973 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_2_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s3_1_GSLv3-7_23_SL87436.fastq.gz fastq fastq 486837300.0 3245582.0 GSM1920165 r3 0:75 1:75 A:133023210;C:110281221;G:109942540;T:133313592;N:276737 75 75     133023210 110281221 109942540 133313592 276737 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92899 0.93046 0.10865 0.10762 0.72072 0.72318 0.48259 0.48426 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40097 40097 SRR2834974 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_2_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s4_1_GSLv3-7_23_SL87436.fastq.gz fastq fastq 485411700.0 3236078.0 GSM1920165 r4 0:75 1:75 A:132626960;C:109930977;G:109581364;T:132961292;N:311107 75 75     132626960 109930977 109581364 132961292 311107 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9286 0.93026 0.10832 0.10644 0.72297 0.72346 0.4874 0.49102 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40098 40098 SRR2834975 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s5_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 487560000.0 3250400.0 GSM1920165 r5 0:75 1:75 A:133286189;C:110453035;G:110087494;T:133554875;N:178407 75 75     133286189 110453035 110087494 133554875 178407 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92891 0.93047 0.10831 0.10771 0.72149 0.7245 0.49325 0.48714 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40099 40099 SRR2834976 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s6_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 486186000.0 3241240.0 GSM1920165 r6 0:75 1:75 A:132920243;C:110179356;G:109765123;T:133207238;N:114040 75 75     132920243 110179356 109765123 133207238 114040 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92939 0.93084 0.1084 0.10801 0.72042 0.72243 0.47565 0.48246 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40100 40100 SRR2834977 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s7_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 488196450.0 3254643.0 GSM1920165 r7 0:75 1:75 A:133435460;C:110572473;G:110204332;T:133803554;N:180631 75 75     133435460 110572473 110204332 133803554 180631 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92819 0.92984 0.10929 0.10799 0.72109 0.72358 0.48011 0.48019 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40101 40101 SRR2834978 SRX1389537 SRS1136858 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 2 GSM1920165   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920165 GSM1920165: 4dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920165   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_23_SL87436.fastq.gz C6E48ANXX_s8_2_GSLv3-7_23_SL87436.fastq.gz fastq fastq 488860050.0 3259067.0 GSM1920165 r8 0:75 1:75 A:133609234;C:110684347;G:110351869;T:134114679;N:99921 75 75     133609234 110684347 110351869 134114679 99921 SRX1389537 SRS1136858 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92896 0.92999 0.1084 0.10803 0.72084 0.72356 0.49134 0.49116 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40102 40102 SRR2834963 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_2_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s1_1_GSLv3-7_22_SL87435.fastq.gz fastq fastq 655472850.0 4369819.0 GSM1920164 r1 0:75 1:75 A:178737627;C:148927106;G:148498282;T:179060826;N:249009 75 75     178737627 148927106 148498282 179060826 249009 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93171 0.93141 0.10054 0.09978 0.72393 0.72346 0.48424 0.48454 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40103 40103 SRR2834964 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s2_2_GSLv3-7_22_SL87435.fastq.gz fastq fastq 653160450.0 4354403.0 GSM1920164 r2 0:75 1:75 A:178133065;C:148392856;G:147908081;T:178504378;N:222070 75 75     178133065 148392856 147908081 178504378 222070 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93192 0.93245 0.10096 0.10045 0.72291 0.72395 0.47919 0.47734 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40104 40104 SRR2834965 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_1_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s3_2_GSLv3-7_22_SL87435.fastq.gz fastq fastq 652456950.0 4349713.0 GSM1920164 r3 0:75 1:75 A:177856950;C:148278733;G:147788506;T:178176744;N:356017 75 75     177856950 148278733 147788506 178176744 356017 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93136 0.93389 0.10164 0.10015 0.72338 0.72295 0.48266 0.48466 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40105 40105 SRR2834966 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_1_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s4_2_GSLv3-7_22_SL87435.fastq.gz fastq fastq 652485450.0 4349903.0 GSM1920164 r4 0:75 1:75 A:177931040;C:148194281;G:147710080;T:178246316;N:403733 75 75     177931040 148194281 147710080 178246316 403733 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93269 0.93166 0.10106 0.09959 0.72125 0.72222 0.47965 0.47865 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40106 40106 SRR2834967 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_2_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s5_1_GSLv3-7_22_SL87435.fastq.gz fastq fastq 654140850.0 4360939.0 GSM1920164 r5 0:75 1:75 A:178373743;C:148681893;G:148154687;T:178701989;N:228538 75 75     178373743 148681893 148154687 178701989 228538 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93158 0.93218 0.10222 0.10131 0.72372 0.72462 0.48616 0.47867 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40107 40107 SRR2834968 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_2_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s6_1_GSLv3-7_22_SL87435.fastq.gz fastq fastq 652504050.0 4350027.0 GSM1920164 r6 0:75 1:75 A:177986433;C:148283047;G:147771732;T:178319277;N:143561 75 75     177986433 148283047 147771732 178319277 143561 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93154 0.9327 0.10219 0.10151 0.72565 0.72553 0.47281 0.47409 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40108 40108 SRR2834969 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s7_2_GSLv3-7_22_SL87435.fastq.gz fastq fastq 656014350.0 4373429.0 GSM1920164 r7 0:75 1:75 A:178923118;C:149044133;G:148505537;T:179300952;N:240610 75 75     178923118 149044133 148505537 179300952 240610 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.93214 0.93328 0.10168 0.10022 0.72439 0.72537 0.48497 0.48467 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40109 40109 SRR2834970 SRX1389536 SRS1136856 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa mRNA rep 1 GSM1920164   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:mRNA 4dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:mRNA GSM1920164 GSM1920164: 4dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920164   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_22_SL87435.fastq.gz C6E48ANXX_s8_2_GSLv3-7_22_SL87435.fastq.gz fastq fastq 656954250.0 4379695.0 GSM1920164 r8 0:75 1:75 A:179194309;C:149203529;G:148721854;T:179702339;N:132219 75 75     179194309 149203529 148721854 179702339 132219 SRX1389536 SRS1136856 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9314 0.93231 0.10013 0.09951 0.72224 0.72291 0.48375 0.48097 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40110 40110 SRR2834955 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s1_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 650372550.0 4335817.0 GSM1920163 r1 0:75 1:75 A:177668824;C:146986894;G:146983667;T:178473980;N:259185 75 75     177668824 146986894 146983667 178473980 259185 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9196 0.91903 0.1135 0.11218 0.73655 0.74123 0.47955 0.48137 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40111 40111 SRR2834956 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s2_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 648743850.0 4324959.0 GSM1920163 r2 0:75 1:75 A:177289639;C:146595379;G:146581079;T:178036595;N:241158 75 75     177289639 146595379 146581079 178036595 241158 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91862 0.92097 0.11152 0.11061 0.73705 0.7402 0.48872 0.48715 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40112 40112 SRR2834957 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s3_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 646270200.0 4308468.0 GSM1920163 r3 0:75 1:75 A:176590169;C:146067441;G:145987115;T:177260606;N:364869 75 75     176590169 146067441 145987115 177260606 364869 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9187 0.92032 0.11196 0.11241 0.73584 0.74044 0.49297 0.48476 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40113 40113 SRR2834958 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s4_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 645048600.0 4300324.0 GSM1920163 r4 0:75 1:75 A:176251571;C:145770742;G:145679733;T:176933493;N:413061 75 75     176251571 145770742 145679733 176933493 413061 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91857 0.92034 0.11121 0.11179 0.73659 0.74065 0.49192 0.4868 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40114 40114 SRR2834959 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s5_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 647546250.0 4316975.0 GSM1920163 r5 0:75 1:75 A:176977558;C:146400262;G:146289490;T:177643963;N:234977 75 75     176977558 146400262 146289490 177643963 234977 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91913 0.92109 0.11107 0.10974 0.73665 0.73971 0.49821 0.48936 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40115 40115 SRR2834960 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s6_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 646175400.0 4307836.0 GSM1920163 r6 0:75 1:75 A:176624846;C:146106353;G:145986272;T:177307724;N:150205 75 75     176624846 146106353 145986272 177307724 150205 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91833 0.92114 0.11161 0.11247 0.7386 0.74002 0.49086 0.48797 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40116 40116 SRR2834961 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s7_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 647806350.0 4318709.0 GSM1920163 r7 0:75 1:75 A:177019815;C:146443925;G:146324420;T:177778409;N:239781 75 75     177019815 146443925 146324420 177778409 239781 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9197 0.92058 0.11188 0.11182 0.7374 0.73979 0.49423 0.49079 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40117 40117 SRR2834962 SRX1389535 SRS1136857 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 3 GSM1920163   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920163 GSM1920163: 0dpa mRNA rep 3; Danio rerio; RNA Seq GSM1920163   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_06_SL87419.fastq.gz C6E48ANXX_s8_2_GSLv3-7_06_SL87419.fastq.gz fastq fastq 650047050.0 4333647.0 GSM1920163 r8 0:75 1:75 A:177656397;C:146865403;G:146748776;T:178644575;N:131899 75 75     177656397 146865403 146748776 178644575 131899 SRX1389535 SRS1136857 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91779 0.92002 0.11203 0.11214 0.73994 0.74304 0.48177 0.4802 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40118 40118 SRR2834947 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s1_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 700436850.0 4669579.0 GSM1920162 r1 0:75 1:75 A:191043526;C:158773140;G:158671547;T:191687156;N:261481 75 75     191043526 158773140 158671547 191687156 261481 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91826 0.92008 0.11155 0.11184 0.73919 0.73931 0.48582 0.4913 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40119 40119 SRR2834948 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s2_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 699345450.0 4662303.0 GSM1920162 r2 0:75 1:75 A:190761312;C:158509623;G:158363841;T:191468510;N:242164 75 75     190761312 158509623 158363841 191468510 242164 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9211 0.9213 0.11139 0.11136 0.73959 0.74176 0.48694 0.48163 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40120 40120 SRR2834949 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s3_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 697996200.0 4653308.0 GSM1920162 r3 0:75 1:75 A:190326358;C:158254512;G:158068949;T:190956016;N:390365 75 75     190326358 158254512 158068949 190956016 390365 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92022 0.92109 0.11237 0.11236 0.74087 0.74115 0.48885 0.48766 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40121 40121 SRR2834950 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s4_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 697694550.0 4651297.0 GSM1920162 r4 0:75 1:75 A:190296982;C:158085077;G:157943995;T:190925028;N:443468 75 75     190296982 158085077 157943995 190925028 443468 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92047 0.92101 0.11316 0.11355 0.74188 0.74117 0.48917 0.48708 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40122 40122 SRR2834951 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s5_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 700187400.0 4667916.0 GSM1920162 r5 0:75 1:75 A:190994041;C:158754310;G:158528600;T:191657174;N:253275 75 75     190994041 158754310 158528600 191657174 253275 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91977 0.92055 0.1126 0.11338 0.73921 0.74162 0.48367 0.48459 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40123 40123 SRR2834952 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s6_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 698374050.0 4655827.0 GSM1920162 r6 0:75 1:75 A:190548226;C:158342206;G:158127659;T:191197694;N:158265 75 75     190548226 158342206 158127659 191197694 158265 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9205 0.92142 0.11195 0.11274 0.74095 0.74182 0.47802 0.48337 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40124 40124 SRR2834953 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s7_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 700600050.0 4670667.0 GSM1920162 r7 0:75 1:75 A:191112928;C:158777843;G:158570917;T:191873256;N:265106 75 75     191112928 158777843 158570917 191873256 265106 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92093 0.92187 0.11199 0.11237 0.73805 0.73882 0.48722 0.49062 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40125 40125 SRR2834954 SRX1389534 SRS1136847 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 2 GSM1920162   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920162 GSM1920162: 0dpa mRNA rep 2; Danio rerio; RNA Seq GSM1920162   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920162 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_05_SL87418.fastq.gz C6E48ANXX_s8_2_GSLv3-7_05_SL87418.fastq.gz fastq fastq 700182000.0 4667880.0 GSM1920162 r8 0:75 1:75 A:191023806;C:158642464;G:158475749;T:191901106;N:138875 75 75     191023806 158642464 158475749 191901106 138875 SRX1389534 SRS1136847 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91882 0.92095 0.11284 0.11365 0.74087 0.74115 0.47214 0.49235 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40126 40126 SRR2834939 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s1_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s1_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 582361950.0 3882413.0 GSM1920161 r1 0:75 1:75 A:158980590;C:131770247;G:131734955;T:159657311;N:218847 75 75     158980590 131770247 131734955 159657311 218847 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91497 0.91586 0.11401 0.11412 0.73689 0.73738 0.49311 0.49105 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40127 40127 SRR2834940 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s2_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s2_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 579950700.0 3866338.0 GSM1920161 r2 0:75 1:75 A:158309372;C:131242268;G:131179210;T:159026086;N:193764 75 75     158309372 131242268 131179210 159026086 193764 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91483 0.91594 0.11629 0.1161 0.73697 0.7361 0.48411 0.48009 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40128 40128 SRR2834941 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s3_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s3_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 580237650.0 3868251.0 GSM1920161 r3 0:75 1:75 A:158383703;C:131297430;G:131223220;T:159013576;N:319721 75 75     158383703 131297430 131223220 159013576 319721 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9145 0.91635 0.11443 0.11498 0.73774 0.73679 0.4824 0.48614 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40129 40129 SRR2834942 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s4_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s4_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 580112100.0 3867414.0 GSM1920161 r4 0:75 1:75 A:158344924;C:131253916;G:131157751;T:158983067;N:372442 75 75     158344924 131253916 131157751 158983067 372442 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91529 0.91522 0.11364 0.11398 0.73669 0.73677 0.48022 0.47541 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40130 40130 SRR2834943 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s5_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s5_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 582177450.0 3881183.0 GSM1920161 r5 0:75 1:75 A:158974316;C:131765407;G:131643906;T:159588423;N:205398 75 75     158974316 131765407 131643906 159588423 205398 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91553 0.91691 0.11598 0.11509 0.73645 0.73559 0.47882 0.48657 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40131 40131 SRR2834944 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s6_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s6_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 581490600.0 3876604.0 GSM1920161 r6 0:75 1:75 A:158768236;C:131623366;G:131503385;T:159464556;N:131057 75 75     158768236 131623366 131503385 159464556 131057 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91423 0.91511 0.11472 0.11497 0.73718 0.73673 0.47432 0.46725 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40132 40132 SRR2834945 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s7_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s7_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 583328400.0 3888856.0 GSM1920161 r7 0:75 1:75 A:159245409;C:131993719;G:131909741;T:159973163;N:206368 75 75     159245409 131993719 131909741 159973163 206368 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91489 0.91558 0.11608 0.11569 0.73565 0.73499 0.48739 0.48871 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40133 40133 SRR2834946 SRX1389533 SRS1136848 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa mRNA rep 1 GSM1920161   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:mRNA 0dpa mRNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:mRNA GSM1920161 GSM1920161: 0dpa mRNA rep 1; Danio rerio; RNA Seq GSM1920161   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP065355     C6E48ANXX_s8_1_GSLv3-7_04_SL87417.fastq.gz C6E48ANXX_s8_2_GSLv3-7_04_SL87417.fastq.gz fastq fastq 583009800.0 3886732.0 GSM1920161 r8 0:75 1:75 A:159196479;C:131874298;G:131794222;T:160029517;N:115284 75 75     159196479 131874298 131794222 160029517 115284 SRX1389533 SRS1136848 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 2 0.91362 0.91467 0.11595 0.1159 0.73596 0.73468 0.4885 0.4884 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40134 40134 SRR2834938 SRX1389532 SRS1136849 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa small RNA rep 3 GSM1920160   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA 4dpa small RNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:small RNA GSM1920160 GSM1920160: 4dpa small RNA rep 3; Danio rerio; RNA Seq GSM1920160   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920160 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     RPD2-A3_ATGTCA_L007_R1_001.fastq.gz fastq 373679650.0 7473593.0 GSM1920160 r1 0:50 A:68694509;C:89847229;G:118844938;T:95955229;N:337745 50       68694509 89847229 118844938 95955229 337745 SRX1389532 SRS1136849 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.11965   0.00285   0.99433   0.52581   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40135 40135 SRR2834937 SRX1389531 SRS1136850 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa small RNA rep 2 GSM1920159   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA 4dpa small RNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:small RNA GSM1920159 GSM1920159: 4dpa small RNA rep 2; Danio rerio; RNA Seq GSM1920159   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920159 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     RPD2-A2_AGTTCC_L007_R1_001.fastq.gz fastq 445390000.0 8907800.0 GSM1920159 r1 0:50 A:81500522;C:106498774;G:142041440;T:114948557;N:400707 50       81500522 106498774 142041440 114948557 400707 SRX1389531 SRS1136850 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.16246   0.00439   0.99506   0.52311   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40136 40136 SRR2834936 SRX1389530 SRS1136851 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   4dpa small RNA rep 1 GSM1920158   source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA 4dpa small RNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:4|library type:small RNA GSM1920158 GSM1920158: 4dpa small RNA rep 1; Danio rerio; RNA Seq GSM1920158   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920158 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     RPD2-A1_AGTCAA_L007_R1_001.fastq.gz fastq 447070900.0 8941418.0 GSM1920158 r1 0:50 A:81330845;C:108093874;G:142869603;T:114376524;N:400054 50       81330845 108093874 142869603 114376524 400054 SRX1389530 SRS1136851 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.19014   0.00382   0.99484   0.52592   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40137 40137 SRR2834935 SRX1389529 SRS1136852 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa small RNA rep 3 GSM1920157   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA 0dpa small RNA rep 3 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:small RNA GSM1920157 GSM1920157: 0dpa small RNA rep 3; Danio rerio; RNA Seq GSM1920157   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920157 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     UPD2-A3_GCCAAT_L007_R1_001.fastq.gz fastq 262275650.0 5245513.0 GSM1920157 r1 0:50 A:50807514;C:65746360;G:82912384;T:62571646;N:237746 50       50807514 65746360 82912384 62571646 237746 SRX1389529 SRS1136852 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.13825   0.00592   0.99401   0.53009   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40138 40138 SRR2834934 SRX1389528 SRS1136853 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa small RNA rep 2 GSM1920156   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA 0dpa small RNA rep 2 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:small RNA GSM1920156 GSM1920156: 0dpa small RNA rep 2; Danio rerio; RNA Seq GSM1920156   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920156 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     UPD2-A2_ACAGTG_L007_R1_001.fastq.gz fastq 754057150.0 15081143.0 GSM1920156 r1 0:50 A:136745812;C:183633004;G:238526597;T:194475603;N:676134 50       136745812 183633004 238526597 194475603 676134 SRX1389528 SRS1136853 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.09694   0.00492   0.99381   0.54425   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure
40139 40139 SRR2834933 SRX1389527 SRS1136854 SRP065355 PRJNA300314 Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration GSE74415 Transcriptome Analysis Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.   pubmed:27355827   0dpa small RNA rep 1 GSM1920155   source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA 0dpa small RNA rep 1 Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample. caudal fin Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222. Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle. tissue:caudal fin|dy post amputation:0|library type:small RNA GSM1920155 GSM1920155: 0dpa small RNA rep 1; Danio rerio; RNA Seq GSM1920155   1 Total RNA was isolated using TRI Reagent Molecular Research Center Inc. Cincinnati OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries. GEO Accession:GSM1920155 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065355     UPD2-A1_TGACCA_L007_R1_001.fastq.gz fastq 617544950.0 12350899.0 GSM1920155 r1 0:50 A:112140176;C:151825965;G:197163658;T:155854533;N:560618 50       112140176 151825965 197163658 155854533 560618 SRX1389527 SRS1136854 SRA307553 GEO Molecular and Biomedical Sciences, University of Maine 1 0.10954   0.00515   0.99295   0.553   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2015-10-27 Adult Adult Fin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;