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
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,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,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,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,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,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
75319,SRR24471179,SRX20257909,SRS17589520,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep3,GSM7306455,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306455,GSM7306455: s1 KO fin 4dpa.rep3; Danio rerio; RNA Seq,GSM7306455 r1,GSM7306455,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,33_s1_KO_fin_4_dpa_L1_1.fq.gz 33_s1_KO_fin_4_dpa_L1_2.fq.gz,fastq fastq,3999247600.0,19996238.0,GSM7306455 r1,0:100 1:100,A:893931840;C:1134885237;G:1020930670;T:949399242;N:100611,100,100,,,893931840,1134885237,1020930670,949399242,100611,SRX20257909,SRS17589520,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.83773,0.84292,0.2627,0.2651,0.86472,0.86214,0.70947,0.70645,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75320,SRR24471180,SRX20257909,SRS17589520,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep3,GSM7306455,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306455,GSM7306455: s1 KO fin 4dpa.rep3; Danio rerio; RNA Seq,GSM7306455 r1,GSM7306455,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,33_s1_KO_fin_4_dpa_L2_1.fq.gz 33_s1_KO_fin_4_dpa_L2_2.fq.gz,fastq fastq,4261340400.0,21306702.0,GSM7306455 r2,0:100 1:100,A:951546226;C:1209228500;G:1090563690;T:1009983924;N:18060,100,100,,,951546226,1209228500,1090563690,1009983924,18060,SRX20257909,SRS17589520,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.83892,0.8426,0.26257,0.26271,0.86409,0.86296,0.71215,0.70859,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75321,SRR24471181,SRX20257908,SRS17589519,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep2,GSM7306454,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306454,GSM7306454: s1 KO fin 4dpa.rep2; Danio rerio; RNA Seq,GSM7306454 r1,GSM7306454,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,32_s1_KO_fin_4_dpa_L1_2.fq.gz 32_s1_KO_fin_4_dpa_L1_1.fq.gz,fastq fastq,3240321800.0,16201609.0,GSM7306454 r1,0:100 1:100,A:723127203;C:912770273;G:835200628;T:769145595;N:78101,100,100,,,723127203,912770273,835200628,769145595,78101,SRX20257908,SRS17589519,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87305,0.87624,0.26972,0.2707,0.84084,0.83855,0.69583,0.69504,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75322,SRR24471182,SRX20257908,SRS17589519,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep2,GSM7306454,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306454,GSM7306454: s1 KO fin 4dpa.rep2; Danio rerio; RNA Seq,GSM7306454 r1,GSM7306454,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,32_s1_KO_fin_4_dpa_L2_2.fq.gz 32_s1_KO_fin_4_dpa_L2_1.fq.gz,fastq fastq,3395022000.0,16975110.0,GSM7306454 r2,0:100 1:100,A:756987332;C:956219461;G:877001998;T:804798936;N:14273,100,100,,,756987332,956219461,877001998,804798936,14273,SRX20257908,SRS17589519,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87513,0.87896,0.26929,0.27049,0.84293,0.84037,0.67282,0.69255,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75323,SRR24471183,SRX20257907,SRS17589518,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep2,GSM7306451,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306451,GSM7306451: s1 KO fin 1dpa.rep2; Danio rerio; RNA Seq,GSM7306451 r1,GSM7306451,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,26_s1_KO_fin_1_dpa_L1_1.fq.gz 26_s1_KO_fin_1_dpa_L1_2.fq.gz,fastq fastq,3737680800.0,18688404.0,GSM7306451 r1,0:100 1:100,A:858060841;C:1029703507;G:942189132;T:907632873;N:94447,100,100,,,858060841,1029703507,942189132,907632873,94447,SRX20257907,SRS17589518,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.88282,0.89185,0.22973,0.23085,0.81499,0.81253,0.64426,0.62722,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75324,SRR24471184,SRX20257907,SRS17589518,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep2,GSM7306451,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306451,GSM7306451: s1 KO fin 1dpa.rep2; Danio rerio; RNA Seq,GSM7306451 r1,GSM7306451,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,26_s1_KO_fin_1_dpa_L2_2.fq.gz 26_s1_KO_fin_1_dpa_L2_1.fq.gz,fastq fastq,3980928000.0,19904640.0,GSM7306451 r2,0:100 1:100,A:912798906;C:1096843947;G:1006189708;T:965079021;N:16418,100,100,,,912798906,1096843947,1006189708,965079021,16418,SRX20257907,SRS17589518,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.8848,0.89326,0.22995,0.2304,0.8187,0.81432,0.61356,0.64565,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75325,SRR24471185,SRX20257906,SRS17589517,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep1,GSM7306453,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306453,GSM7306453: s1 KO fin 4dpa.rep1; Danio rerio; RNA Seq,GSM7306453 r1,GSM7306453,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,31_s1_KO_fin_4_dpa_L1_1.fq.gz 31_s1_KO_fin_4_dpa_L1_2.fq.gz,fastq fastq,3467981200.0,17339906.0,GSM7306453 r1,0:100 1:100,A:778024147;C:969670649;G:892069174;T:828128122;N:89108,100,100,,,778024147,969670649,892069174,828128122,89108,SRX20257906,SRS17589517,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.89266,0.89923,0.27513,0.27922,0.83252,0.83067,0.65794,0.65716,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75326,SRR24471186,SRX20257906,SRS17589517,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 4dpa.rep1,GSM7306453,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa|geo loc name:missing|collection date:missing,s1 KO fin 4dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:4dpa,GSM7306453,GSM7306453: s1 KO fin 4dpa.rep1; Danio rerio; RNA Seq,GSM7306453 r1,GSM7306453,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,31_s1_KO_fin_4_dpa_L2_1.fq.gz 31_s1_KO_fin_4_dpa_L2_2.fq.gz,fastq fastq,3678808000.0,18394040.0,GSM7306453 r2,0:100 1:100,A:824384498;C:1028904706;G:948630343;T:876873161;N:15292,100,100,,,824384498,1028904706,948630343,876873161,15292,SRX20257906,SRS17589517,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.89368,0.90041,0.27586,0.27697,0.83544,0.8322,0.66877,0.636,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75327,SRR24471189,SRX20257905,SRS17589516,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep3,GSM7306452,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306452,GSM7306452: s1 KO fin 1dpa.rep3; Danio rerio; RNA Seq,GSM7306452 r1,GSM7306452,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,27_s1_KO_fin_1_dpa_L1_2.fq.gz 27_s1_KO_fin_1_dpa_L1_1.fq.gz,fastq fastq,3468783000.0,17343915.0,GSM7306452 r1,0:100 1:100,A:781608606;C:968943963;G:885159160;T:832982387;N:88884,100,100,,,781608606,968943963,885159160,832982387,88884,SRX20257905,SRS17589516,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.88132,0.88859,0.23585,0.23869,0.83325,0.83082,0.67964,0.66822,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75328,SRR24471190,SRX20257905,SRS17589516,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep3,GSM7306452,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306452,GSM7306452: s1 KO fin 1dpa.rep3; Danio rerio; RNA Seq,GSM7306452 r1,GSM7306452,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,27_s1_KO_fin_1_dpa_L2_1.fq.gz 27_s1_KO_fin_1_dpa_L2_2.fq.gz,fastq fastq,3676314000.0,18381570.0,GSM7306452 r2,0:100 1:100,A:827353354;C:1027223250;G:940534359;T:881187758;N:15279,100,100,,,827353354,1027223250,940534359,881187758,15279,SRX20257905,SRS17589516,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.88203,0.88908,0.23749,0.23797,0.83205,0.82972,0.67783,0.6573,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75329,SRR24471187,SRX20257904,SRS17589515,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep1,GSM7306450,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306450,GSM7306450: s1 KO fin 1dpa.rep1; Danio rerio; RNA Seq,GSM7306450 r1,GSM7306450,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,25_s1_KO_fin_1_dpa_L1_1.fq.gz 25_s1_KO_fin_1_dpa_L1_2.fq.gz,fastq fastq,3002663200.0,15013316.0,GSM7306450 r1,0:100 1:100,A:753436685;C:767699098;G:684677146;T:796774576;N:75695,100,100,,,753436685,767699098,684677146,796774576,75695,SRX20257904,SRS17589515,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87584,0.89018,0.09708,0.09902,0.77589,0.77469,0.56032,0.54604,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75330,SRR24471188,SRX20257904,SRS17589515,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 1dpa.rep1,GSM7306450,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa|geo loc name:missing|collection date:missing,s1 KO fin 1dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:1dpa,GSM7306450,GSM7306450: s1 KO fin 1dpa.rep1; Danio rerio; RNA Seq,GSM7306450 r1,GSM7306450,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,25_s1_KO_fin_1_dpa_L2_1.fq.gz 25_s1_KO_fin_1_dpa_L2_2.fq.gz,fastq fastq,3139845800.0,15699229.0,GSM7306450 r2,0:100 1:100,A:787928979;C:802380571;G:717092839;T:832430033;N:13378,100,100,,,787928979,802380571,717092839,832430033,13378,SRX20257904,SRS17589515,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87449,0.88869,0.09677,0.09885,0.7751,0.77319,0.55363,0.54176,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75331,SRR24471191,SRX20257903,SRS17589514,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep3,GSM7306449,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306449,GSM7306449: s1 KO fin 0dpa.rep3; Danio rerio; RNA Seq,GSM7306449 r1,GSM7306449,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,21_s1_KO_fin_0_dpa_L1_1.fq.gz 21_s1_KO_fin_0_dpa_L1_2.fq.gz,fastq fastq,4647376200.0,23236881.0,GSM7306449 r1,0:100 1:100,A:1184413371;C:1154916070;G:1074813068;T:1233114610;N:119081,100,100,,,1184413371,1154916070,1074813068,1233114610,119081,SRX20257903,SRS17589514,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84382,0.87403,0.14899,0.15267,0.79935,0.79513,0.59784,0.60172,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75332,SRR24471192,SRX20257903,SRS17589514,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep3,GSM7306449,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306449,GSM7306449: s1 KO fin 0dpa.rep3; Danio rerio; RNA Seq,GSM7306449 r1,GSM7306449,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,21_s1_KO_fin_0_dpa_L2_1.fq.gz 21_s1_KO_fin_0_dpa_L2_2.fq.gz,fastq fastq,5003838000.0,25019190.0,GSM7306449 r2,0:100 1:100,A:1274691496;C:1243030235;G:1160163118;T:1325934412;N:18739,100,100,,,1274691496,1243030235,1160163118,1325934412,18739,SRX20257903,SRS17589514,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84422,0.87469,0.14858,0.15129,0.79896,0.79606,0.58866,0.6067,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75333,SRR24471193,SRX20257902,SRS17589513,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep3,GSM7306446,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306446,GSM7306446: WT fin 4dpa.rep3; Danio rerio; RNA Seq,GSM7306446 r1,GSM7306446,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,30_WT_fin_4_dpa_L1_1.fq.gz 30_WT_fin_4_dpa_L1_2.fq.gz,fastq fastq,2895703800.0,14478519.0,GSM7306446 r1,0:100 1:100,A:637271323;C:821976194;G:761589917;T:674794769;N:71597,100,100,,,637271323,821976194,761589917,674794769,71597,SRX20257902,SRS17589513,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.86333,0.8655,0.27657,0.27567,0.87744,0.87592,0.71883,0.68094,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75334,SRR24471194,SRX20257902,SRS17589513,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep3,GSM7306446,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306446,GSM7306446: WT fin 4dpa.rep3; Danio rerio; RNA Seq,GSM7306446 r1,GSM7306446,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,30_WT_fin_4_dpa_L2_2.fq.gz 30_WT_fin_4_dpa_L2_1.fq.gz,fastq fastq,3035028200.0,15175141.0,GSM7306446 r2,0:100 1:100,A:667318836;C:861528893;G:799981189;T:706186665;N:12617,100,100,,,667318836,861528893,799981189,706186665,12617,SRX20257902,SRS17589513,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.86425,0.86576,0.27591,0.27499,0.87787,0.87651,0.69569,0.69298,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75335,SRR24471195,SRX20257901,SRS17589512,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep2,GSM7306448,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306448,GSM7306448: s1 KO fin 0dpa.rep2; Danio rerio; RNA Seq,GSM7306448 r1,GSM7306448,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,20_s1_KO_fin_0_dpa_L1_1.fq.gz 20_s1_KO_fin_0_dpa_L1_2.fq.gz,fastq fastq,3889366400.0,19446832.0,GSM7306448 r1,0:100 1:100,A:1011531085;C:944363900;G:889149542;T:1044223628;N:98245,100,100,,,1011531085,944363900,889149542,1044223628,98245,SRX20257901,SRS17589512,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85286,0.88229,0.06794,0.06868,0.81832,0.81602,0.58944,0.59087,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75336,SRR24471196,SRX20257901,SRS17589512,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep2,GSM7306448,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306448,GSM7306448: s1 KO fin 0dpa.rep2; Danio rerio; RNA Seq,GSM7306448 r1,GSM7306448,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,20_s1_KO_fin_0_dpa_L2_1.fq.gz 20_s1_KO_fin_0_dpa_L2_2.fq.gz,fastq fastq,4129723600.0,20648618.0,GSM7306448 r2,0:100 1:100,A:1074214836;C:1001933315;G:945467504;T:1108091908;N:16037,100,100,,,1074214836,1001933315,945467504,1108091908,16037,SRX20257901,SRS17589512,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85277,0.88156,0.06848,0.06862,0.81749,0.81633,0.58456,0.57082,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75337,SRR24471199,SRX20257900,SRS17589511,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep1,GSM7306447,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306447,GSM7306447: s1 KO fin 0dpa.rep1; Danio rerio; RNA Seq,GSM7306447 r1,GSM7306447,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,19_s1_KO_fin_0_dpa_L1_2.fq.gz 19_s1_KO_fin_0_dpa_L1_1.fq.gz,fastq fastq,5408284200.0,27041421.0,GSM7306447 r1,0:100 1:100,A:1335394300;C:1383591861;G:1296375171;T:1392781925;N:140943,100,100,,,1335394300,1383591861,1296375171,1392781925,140943,SRX20257900,SRS17589511,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.83536,0.85442,0.20782,0.20942,0.80273,0.80008,0.57991,0.60869,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75338,SRR24471200,SRX20257900,SRS17589511,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,s1 KO fin 0dpa.rep1,GSM7306447,,source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing,s1 KO fin 0dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa,GSM7306447,GSM7306447: s1 KO fin 0dpa.rep1; Danio rerio; RNA Seq,GSM7306447 r1,GSM7306447,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,19_s1_KO_fin_0_dpa_L2_2.fq.gz 19_s1_KO_fin_0_dpa_L2_1.fq.gz,fastq fastq,5769810600.0,28849053.0,GSM7306447 r2,0:100 1:100,A:1423191820;C:1476436717;G:1387044625;T:1483114596;N:22842,100,100,,,1423191820,1476436717,1387044625,1483114596,22842,SRX20257900,SRS17589511,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.83565,0.85491,0.20621,0.20907,0.80119,0.79951,0.57335,0.59059,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75339,SRR24471197,SRX20257899,SRS17589510,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep2,GSM7306445,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306445,GSM7306445: WT fin 4dpa.rep2; Danio rerio; RNA Seq,GSM7306445 r1,GSM7306445,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,29_WT_fin_4_dpa_L1_1.fq.gz 29_WT_fin_4_dpa_L1_2.fq.gz,fastq fastq,3538892400.0,17694462.0,GSM7306445 r1,0:100 1:100,A:776735645;C:1003894878;G:937502302;T:820668728;N:90847,100,100,,,776735645,1003894878,937502302,820668728,90847,SRX20257899,SRS17589510,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85515,0.85413,0.2763,0.27403,0.89301,0.89254,0.72567,0.72364,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75340,SRR24471198,SRX20257899,SRS17589510,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep2,GSM7306445,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306445,GSM7306445: WT fin 4dpa.rep2; Danio rerio; RNA Seq,GSM7306445 r1,GSM7306445,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,29_WT_fin_4_dpa_L2_1.fq.gz 29_WT_fin_4_dpa_L2_2.fq.gz,fastq fastq,3788355000.0,18941775.0,GSM7306445 r2,0:100 1:100,A:830384900;C:1074966039;G:1006176464;T:876812492;N:15105,100,100,,,830384900,1074966039,1006176464,876812492,15105,SRX20257899,SRS17589510,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85797,0.85587,0.27582,0.27417,0.89589,0.89471,0.67475,0.72233,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75341,SRR24471201,SRX20257898,SRS17589509,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep1,GSM7306444,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306444,GSM7306444: WT fin 4dpa.rep1; Danio rerio; RNA Seq,GSM7306444 r1,GSM7306444,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,28_WT_fin_4_dpa_L1_1.fq.gz 28_WT_fin_4_dpa_L1_2.fq.gz,fastq fastq,2986096200.0,14930481.0,GSM7306444 r1,0:100 1:100,A:658917203;C:844259999;G:789571843;T:693271016;N:76139,100,100,,,658917203,844259999,789571843,693271016,76139,SRX20257898,SRS17589509,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85443,0.85474,0.27304,0.27253,0.88631,0.88538,0.69497,0.71131,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75342,SRR24471202,SRX20257898,SRS17589509,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 4dpa.rep1,GSM7306444,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:4dpa|geo loc name:missing|collection date:missing,WT fin 4dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:4dpa,GSM7306444,GSM7306444: WT fin 4dpa.rep1; Danio rerio; RNA Seq,GSM7306444 r1,GSM7306444,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,28_WT_fin_4_dpa_L2_1.fq.gz 28_WT_fin_4_dpa_L2_2.fq.gz,fastq fastq,3224172600.0,16120863.0,GSM7306444 r2,0:100 1:100,A:710701776;C:911709616;G:854517979;T:747230665;N:12564,100,100,,,710701776,911709616,854517979,747230665,12564,SRX20257898,SRS17589509,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.85381,0.85466,0.27146,0.27186,0.887,0.88607,0.71477,0.71165,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75343,SRR24471203,SRX20257897,SRS17589508,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep1,GSM7306441,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306441,GSM7306441: WT fin 1dpa.rep1; Danio rerio; RNA Seq,GSM7306441 r1,GSM7306441,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,22_WT_fin_1_dpa_L1_1.fq.gz 22_WT_fin_1_dpa_L1_2.fq.gz,fastq fastq,3427935400.0,17139677.0,GSM7306441 r1,0:100 1:100,A:802598864;C:925555668;G:848618771;T:851075644;N:86453,100,100,,,802598864,925555668,848618771,851075644,86453,SRX20257897,SRS17589508,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87193,0.88185,0.20566,0.20837,0.79983,0.79691,0.60706,0.60178,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75344,SRR24471204,SRX20257897,SRS17589508,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep1,GSM7306441,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306441,GSM7306441: WT fin 1dpa.rep1; Danio rerio; RNA Seq,GSM7306441 r1,GSM7306441,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,22_WT_fin_1_dpa_L2_1.fq.gz 22_WT_fin_1_dpa_L2_2.fq.gz,fastq fastq,3638002200.0,18190011.0,GSM7306441 r2,0:100 1:100,A:851083615;C:982445301;G:902716257;T:901741743;N:15284,100,100,,,851083615,982445301,902716257,901741743,15284,SRX20257897,SRS17589508,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87549,0.88289,0.205,0.20692,0.79717,0.7949,0.58335,0.59027,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75345,SRR24471205,SRX20257896,SRS17589507,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep3,GSM7306443,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306443,GSM7306443: WT fin 1dpa.rep3; Danio rerio; RNA Seq,GSM7306443 r1,GSM7306443,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,24_WT_fin_1_dpa_L1_1.fq.gz 24_WT_fin_1_dpa_L1_2.fq.gz,fastq fastq,3379919400.0,16899597.0,GSM7306443 r1,0:100 1:100,A:755985358;C:948096692;G:872436341;T:803315260;N:85749,100,100,,,755985358,948096692,872436341,803315260,85749,SRX20257896,SRS17589507,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84706,0.85026,0.25126,0.25353,0.85423,0.85188,0.62099,0.69433,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75346,SRR24471206,SRX20257896,SRS17589507,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep3,GSM7306443,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306443,GSM7306443: WT fin 1dpa.rep3; Danio rerio; RNA Seq,GSM7306443 r1,GSM7306443,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,24_WT_fin_1_dpa_L2_1.fq.gz 24_WT_fin_1_dpa_L2_2.fq.gz,fastq fastq,3608476600.0,18042383.0,GSM7306443 r2,0:100 1:100,A:806268395;C:1012102898;G:934107839;T:855982694;N:14774,100,100,,,806268395,1012102898,934107839,855982694,14774,SRX20257896,SRS17589507,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84901,0.85169,0.25136,0.25119,0.85598,0.85385,0.67921,0.66771,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75347,SRR24471209,SRX20257895,SRS17589506,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep2,GSM7306442,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306442,GSM7306442: WT fin 1dpa.rep2; Danio rerio; RNA Seq,GSM7306442 r1,GSM7306442,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,23_WT_fin_1_dpa_L1_1.fq.gz 23_WT_fin_1_dpa_L1_2.fq.gz,fastq fastq,3619024800.0,18095124.0,GSM7306442 r1,0:100 1:100,A:863317631;C:968246576;G:885432283;T:901937647;N:90663,100,100,,,863317631,968246576,885432283,901937647,90663,SRX20257895,SRS17589506,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87193,0.88512,0.19894,0.20141,0.79299,0.79086,0.63119,0.63234,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75348,SRR24471210,SRX20257895,SRS17589506,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 1dpa.rep2,GSM7306442,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:1dpa|geo loc name:missing|collection date:missing,WT fin 1dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:1dpa,GSM7306442,GSM7306442: WT fin 1dpa.rep2; Danio rerio; RNA Seq,GSM7306442 r1,GSM7306442,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,23_WT_fin_1_dpa_L2_1.fq.gz 23_WT_fin_1_dpa_L2_2.fq.gz,fastq fastq,3827008200.0,19135041.0,GSM7306442 r2,0:100 1:100,A:912017066;C:1024127984;G:938443774;T:952403081;N:16295,100,100,,,912017066,1024127984,938443774,952403081,16295,SRX20257895,SRS17589506,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.87306,0.88517,0.19735,0.19972,0.79364,0.79007,0.62221,0.62995,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75349,SRR24471207,SRX20257894,SRS17589505,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep3,GSM7306440,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306440,GSM7306440: WT fin 0dpa.rep3; Danio rerio; RNA Seq,GSM7306440 r1,GSM7306440,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,18_WT_fin_0_dpa_L1_2.fq.gz 18_WT_fin_0_dpa_L1_1.fq.gz,fastq fastq,4291096400.0,21455482.0,GSM7306440 r1,0:100 1:100,A:1110083597;C:1052453707;G:974792610;T:1153671168;N:95318,100,100,,,1110083597,1052453707,974792610,1153671168,95318,SRX20257894,SRS17589505,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84606,0.87686,0.0768,0.07671,0.8084,0.80273,0.58076,0.5308,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75350,SRR24471208,SRX20257894,SRS17589505,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep3,GSM7306440,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep3,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306440,GSM7306440: WT fin 0dpa.rep3; Danio rerio; RNA Seq,GSM7306440 r1,GSM7306440,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,18_WT_fin_0_dpa_L2_2.fq.gz 18_WT_fin_0_dpa_L2_1.fq.gz,fastq fastq,4628716600.0,23143583.0,GSM7306440 r2,0:100 1:100,A:1199182064;C:1132323689;G:1052169965;T:1245025229;N:15653,100,100,,,1199182064,1132323689,1052169965,1245025229,15653,SRX20257894,SRS17589505,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84542,0.87681,0.07732,0.07719,0.80894,0.80111,0.56736,0.58901,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75351,SRR24471211,SRX20257893,SRS17589504,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep2,GSM7306439,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306439,GSM7306439: WT fin 0dpa.rep2; Danio rerio; RNA Seq,GSM7306439 r1,GSM7306439,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,17_WT_fin_0_dpa_L1_1.fq.gz 17_WT_fin_0_dpa_L1_2.fq.gz,fastq fastq,3460056800.0,17300284.0,GSM7306439 r1,0:100 1:100,A:908351067;C:835549646;G:781551673;T:934516356;N:88058,100,100,,,908351067,835549646,781551673,934516356,88058,SRX20257893,SRS17589504,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.83921,0.87723,0.07173,0.07272,0.8127,0.81024,0.57558,0.5823,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75352,SRR24471212,SRX20257893,SRS17589504,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep2,GSM7306439,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep2,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306439,GSM7306439: WT fin 0dpa.rep2; Danio rerio; RNA Seq,GSM7306439 r1,GSM7306439,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,17_WT_fin_0_dpa_L2_1.fq.gz 17_WT_fin_0_dpa_L2_2.fq.gz,fastq fastq,3681349600.0,18406748.0,GSM7306439 r2,0:100 1:100,A:966553966;C:888292123;G:832617682;T:993871075;N:14754,100,100,,,966553966,888292123,832617682,993871075,14754,SRX20257893,SRS17589504,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84019,0.87738,0.07212,0.07365,0.81134,0.80848,0.56863,0.57674,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75353,SRR24471213,SRX20257892,SRS17589503,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep1,GSM7306438,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306438,GSM7306438: WT fin 0dpa.rep1; Danio rerio; RNA Seq,GSM7306438 r1,GSM7306438,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,16_WT_fin_0_dpa_L1_1.fq.gz 16_WT_fin_0_dpa_L1_2.fq.gz,fastq fastq,5093515600.0,25467578.0,GSM7306438 r1,0:100 1:100,A:1310664044;C:1254153763;G:1166075927;T:1362496839;N:125027,100,100,,,1310664044,1254153763,1166075927,1362496839,125027,SRX20257892,SRS17589503,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84399,0.86819,0.18135,0.18646,0.7839,0.78216,0.59839,0.58616,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure
75354,SRR24471214,SRX20257892,SRS17589503,SRP436517,PRJNA970301,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes,GSE231956,Transcriptome Analysis,Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.,,pubmed:38290519,,WT fin 0dpa.rep1,GSM7306438,,source name:caudal fin|tissue:caudal fin|genotype:Ekkwill|time:0dpa|geo loc name:missing|collection date:missing,WT fin 0dpa.rep1,RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size,caudal fin,Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.,tissue:caudal fin|genotype:Ekkwill|time:0dpa,GSM7306438,GSM7306438: WT fin 0dpa.rep1; Danio rerio; RNA Seq,GSM7306438 r1,GSM7306438,1,Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP436517,,,16_WT_fin_0_dpa_L2_1.fq.gz 16_WT_fin_0_dpa_L2_2.fq.gz,fastq fastq,5349264600.0,26746323.0,GSM7306438 r2,0:100 1:100,A:1376841457;C:1315997079;G:1226294065;T:1430110380;N:21619,100,100,,,1376841457,1315997079,1226294065,1430110380,21619,SRX20257892,SRS17589503,SRA1634637,"Poss, Cell Biology, Duke University","Poss, Cell Biology, Duke University",2,0.84363,0.86698,0.1813,0.18584,0.78232,0.7809,0.59478,0.60554,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-05-08,Adult,Adult,Fin,Surface Structure