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
33934,SRR30947094,SRX26349630,SRS22874784,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #3,GSM8565205,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #3,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565205,GSM8565205: whole heart  tak1+/+ wild type  replicate #3; Danio rerio; RNA Seq,GSM8565205 r1,GSM8565205,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_3_1.fq.gz WT_3_2.fq.gz,fastq fastq,4449566200.0,22247831.0,GSM8565205 r1,0:100 1:100,A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0,100,100,,,1179341017,1046638560,1046356098,1177230525,0,SRX26349630,SRS22874784,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33935,SRR30947095,SRX26349629,SRS22874783,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #2,GSM8565204,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #2,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565204,GSM8565204: whole heart  tak1+/+ wild type  replicate #2; Danio rerio; RNA Seq,GSM8565204 r1,GSM8565204,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_2_1.fq.gz WT_2_2.fq.gz,fastq fastq,4519627600.0,22598138.0,GSM8565204 r1,0:100 1:100,A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0,100,100,,,1207344552,1055139553,1056806709,1200336786,0,SRX26349629,SRS22874783,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33936,SRR30947096,SRX26349628,SRS22874781,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #1,GSM8565203,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #1,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565203,GSM8565203: whole heart  tak1+/+ wild type  replicate #1; Danio rerio; RNA Seq,GSM8565203 r1,GSM8565203,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_1_1.fq.gz WT_1_2.fq.gz,fastq fastq,4496601200.0,22483006.0,GSM8565203 r1,0:100 1:100,A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0,100,100,,,1201390946,1050348674,1051355386,1193506194,0,SRX26349628,SRS22874781,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33937,SRR30947097,SRX26349627,SRS22874780,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #3,GSM8565202,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #3,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565202,GSM8565202: whole heart  tak1 /  mutant  replicate #3; Danio rerio; RNA Seq,GSM8565202 r1,GSM8565202,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_3_1.fq.gz mut_3_2.fq.gz,fastq fastq,4451759600.0,22258798.0,GSM8565202 r1,0:100 1:100,A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0,100,100,,,1167798041,1064608876,1066460994,1152891689,0,SRX26349627,SRS22874780,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33938,SRR30947098,SRX26349626,SRS22874782,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #2,GSM8565201,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #2,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565201,GSM8565201: whole heart  tak1 /  mutant  replicate #2; Danio rerio; RNA Seq,GSM8565201 r1,GSM8565201,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_2_1.fq.gz mut_2_2.fq.gz,fastq fastq,4534495200.0,22672476.0,GSM8565201 r1,,,,,,,,,,,,SRX26349626,SRS22874782,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33939,SRR30947099,SRX26349625,SRS22874779,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #1,GSM8565200,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #1,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565200,GSM8565200: whole heart  tak1 /  mutant  replicate #1; Danio rerio; RNA Seq,GSM8565200 r1,GSM8565200,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_1_1.fq.gz mut_1_2.fq.gz,fastq fastq,4425052600.0,22125263.0,GSM8565200 r1,0:100 1:100,A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0,100,100,,,1161989932,1055452567,1055912540,1151697561,0,SRX26349625,SRS22874779,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
74329,SRR23635030,SRX19518333,SRS16905710,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,Transcriptome Analysis,Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader”  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,KO  replicate 2  bulk RNAseq,GSM7067524,,source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing,KO  replicate 2  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out,GSM7067524,GSM7067524: KO  replicate 2  bulk RNAseq; Danio rerio; RNA Seq,GSM7067524 r1,GSM7067524,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,KO2.fastq.gz,fastq,4188284200.0,41882842.0,GSM7067524 r1,0:100,A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676,100,,,,1066992737,1011357361,1055554148,1041284278,13095676,SRX19518333,SRS16905710,SRA1597336,Yunnan University,Yunnan University,1,0.88647,,0.07541,,0.7237,,0.47069,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74330,SRR23635031,SRX19518332,SRS16905709,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,Transcriptome Analysis,Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader”  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,KO  replicate 1  bulk RNAseq,GSM7067523,,source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing,KO  replicate 1  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out,GSM7067523,GSM7067523: KO  replicate 1  bulk RNAseq; Danio rerio; RNA Seq,GSM7067523 r1,GSM7067523,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,KO1.fastq.gz,fastq,4181083400.0,41810834.0,GSM7067523 r1,0:100,A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586,100,,,,1077414361,996554293,1053357384,1040649776,13107586,SRX19518332,SRS16905709,SRA1597336,Yunnan University,Yunnan University,1,0.87685,,0.07522,,0.72699,,0.48859,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74331,SRR23635032,SRX19518331,SRS16905708,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,Transcriptome Analysis,Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader”  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,WT  replicate 2  bulk RNAseq,GSM7067522,,source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing,WT  replicate 2  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:wild type,GSM7067522,GSM7067522: WT  replicate 2  bulk RNAseq; Danio rerio; RNA Seq,GSM7067522 r1,GSM7067522,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,WT2.fastq.gz,fastq,1435167700.0,14351677.0,GSM7067522 r1,0:100,A:371412640;C:334204906;G:351277070;T:371684263;N:6588821,100,,,,371412640,334204906,351277070,371684263,6588821,SRX19518331,SRS16905708,SRA1597336,Yunnan University,Yunnan University,1,0.83841,,0.15087,,0.71417,,0.50982,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74332,SRR23635033,SRX19518330,SRS16905707,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,Transcriptome Analysis,Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader”  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,WT  replicate 1  bulk RNAseq,GSM7067521,,source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing,WT  replicate 1  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:wild type,GSM7067521,GSM7067521: WT  replicate 1  bulk RNAseq; Danio rerio; RNA Seq,GSM7067521 r1,GSM7067521,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,WT1.fastq.gz,fastq,1961618800.0,19616188.0,GSM7067521 r1,0:100,A:518460045;C:447438337;G:477081234;T:509513188;N:9125996,100,,,,518460045,447438337,477081234,509513188,9125996,SRX19518330,SRS16905707,SRA1597336,Yunnan University,Yunnan University,1,0.81315,,0.14097,,0.72342,,0.50905,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
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