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
53587,SRR11886668,SRX8434202,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R3,L34024,L34024,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_GCCAAT.fastq.gz,fastq,1907555958.0,37403058.0,ws 3 1 GCCAAT.fastq.gz,0:51 1:0,A:417030128;C:470533688;G:468961155;T:550856047;N:174940,51,0,,,417030128,470533688,468961155,550856047,174940,SRX8434202,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.96213,,0.05602,,0.72967,,0.45848,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53588,SRR11886669,SRX8434201,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R2,L34023,L34023,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_ACAGTG.fastq.gz,fastq,1731933225.0,33959475.0,ws 3 1 ACAGTG.fastq.gz,0:51 1:0,A:381487795;C:424246634;G:426026749;T:500012138;N:159909,51,0,,,381487795,424246634,426026749,500012138,159909,SRX8434201,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.96269,,0.05578,,0.73261,,0.45837,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53589,SRR11886671,SRX8434200,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R1,L34022,L34022,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_TGACCA.fastq.gz,fastq,1814021907.0,35569057.0,ws 3 1 TGACCA.fastq.gz,0:51 1:0,A:404693395;C:438897306;G:444600496;T:525663505;N:167205,51,0,,,404693395,438897306,444600496,525663505,167205,SRX8434200,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95686,,0.06383,,0.72677,,0.44564,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53590,SRR11886672,SRX8434199,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R3,L34021,L34021,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_TTAGGC.fastq.gz,fastq,1894657395.0,37150145.0,ws 3 1 TTAGGC.fastq.gz,0:51 1:0,A:424630121;C:461337738;G:460024108;T:548490887;N:174541,51,0,,,424630121,461337738,460024108,548490887,174541,SRX8434199,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.9524,,0.08535,,0.70999,,0.44299,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53591,SRR11886673,SRX8434198,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R2,L34020,L34020,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_CGATGT.fastq.gz,fastq,1826016036.0,35804236.0,ws 3 1 CGATGT.fastq.gz,0:51 1:0,A:408512993;C:445830968;G:443573205;T:527930321;N:168549,51,0,,,408512993,445830968,443573205,527930321,168549,SRX8434198,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95224,,0.08373,,0.70934,,0.45345,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53592,SRR11886674,SRX8434197,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R1,L34019,L34019,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_ATCACG.fastq.gz,fastq,1889698206.0,37052906.0,ws 3 1 ATCACG.fastq.gz,0:51 1:0,A:425019592;C:459513661;G:459679307;T:545311781;N:173865,51,0,,,425019592,459513661,459679307,545311781,173865,SRX8434197,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95224,,0.08995,,0.71106,,0.45283,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53593,SRR11886700,SRX8434172,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish blastema single cell,L41598,L41598,The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,loader:fastq load.py,L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,52222012142.0,411196946.0,L41598 S1 L001 I1 001.fastq.gz,0:8 1:28 2:91,A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569,8,28,91,,10978857897,7760934381,8557391299,10029401940,92336569,SRX8434172,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.92629,,0.12539,,0.78589,,0.5225,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2020-08-11,Adult,Adult,Fin,Surface Structure