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
173,DRR075397,DRX069311,DRS075492,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of control fish 7dpf,Control body,SAMD00065411,,sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065411,DRX069311,Control body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065411,,,,2653100352.0,73697232.0,DRR075397,0:36,A:656791658;C:620507513;G:625038612;T:750671135;N:91434,36,,,,656791658,620507513,625038612,750671135,91434,DRX069311,DRS075492,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89666,,0.15749,,0.67048,,0.47755,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Trunk,Surface Structure
34548,SRR32104353,SRX27449957,SRS23876478,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 3,GSM8751790,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 3,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751790,GSM8751790: 24hpf TrunkNC 3; Danio rerio; RNA Seq,GSM8751790 r1,GSM8751790,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+3_Trunk_24h_19733_R1_combined_filtered.fastq.gz,fastq,1792416000.0,35848320.0,GSM8751790 r1,0:50,A:512975947;C:383333260;G:389199848;T:506816777;N:90168,50,,,,512975947,383333260,389199848,506816777,90168,SRX27449957,SRS23876478,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
34549,SRR32104354,SRX27449956,SRS23876477,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 2,GSM8751789,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 2,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751789,GSM8751789: 24hpf TrunkNC 2; Danio rerio; RNA Seq,GSM8751789 r1,GSM8751789,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+2_Trunk_24h_19731_R1_combined_filtered.fastq.gz,fastq,1952754850.0,39055097.0,GSM8751789 r1,0:50,A:559564208;C:417671563;G:422591454;T:552829965;N:97660,50,,,,559564208,417671563,422591454,552829965,97660,SRX27449956,SRS23876477,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
34550,SRR32104355,SRX27449955,SRS23876476,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 1,GSM8751788,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 1,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751788,GSM8751788: 24hpf TrunkNC 1; Danio rerio; RNA Seq,GSM8751788 r1,GSM8751788,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+1_Trunk_24h_19729_R1_combined_filtered.fastq.gz,fastq,2086584450.0,41731689.0,GSM8751788 r1,0:50,A:588802695;C:455146722;G:460260703;T:582270728;N:103602,50,,,,588802695,455146722,460260703,582270728,103602,SRX27449955,SRS23876476,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
39771,SRR2136297,SRX1125768,SRS1017739,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Qkiac 3,GSM1838798,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,Qkiac 3,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,GSM1838798,GSM1838798: Qkiac 3; Danio rerio; RNA Seq,GSM1838798,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838798,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample6_CTTGTA.fastq.bz2,fastq,2507001849.0,49156899.0,GSM1838798 r1,0:51,A:683306529;C:570965534;G:570449436;T:679826815;N:2453535,51,,,,683306529,570965534,570449436,679826815,2453535,SRX1125768,SRS1017739,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.92678,,0.08779,,0.72892,,0.48795,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
39772,SRR2136296,SRX1125767,SRS1017740,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Qkiac 2,GSM1838797,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,Qkiac 2,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,GSM1838797,GSM1838797: Qkiac 2; Danio rerio; RNA Seq,GSM1838797,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838797,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample5_CAGATC.fastq.bz2,fastq,2850272086.0,55887688.0,GSM1838797 r1,0:51.00,A:775475703;C:648531668;G:652753738;T:770730439;N:2780538,51,,,,775475703,648531668,652753738,770730439,2780538,SRX1125767,SRS1017740,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.92802,,0.08465,,0.72744,,0.48656,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
39773,SRR2136295,SRX1125766,SRS1017741,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Qkiac 1,GSM1838796,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,Qkiac 1,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino,GSM1838796,GSM1838796: Qkiac 1; Danio rerio; RNA Seq,GSM1838796,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838796,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample4_GCCAAT.fastq.bz2,fastq,2881827420.0,56506420.0,GSM1838796 r1,0:51,A:782512581;C:658453854;G:659856487;T:778195522;N:2808976,51,,,,782512581,658453854,659856487,778195522,2808976,SRX1125766,SRS1017741,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.92629,,0.08316,,0.7276,,0.47801,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
39774,SRR2136294,SRX1125765,SRS1017742,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Control 3,GSM1838795,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,Control 3,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,GSM1838795,GSM1838795: Control 3; Danio rerio; RNA Seq,GSM1838795,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838795,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample3_ACAGTG.fastq.bz2,fastq,2611892782.0,51213584.0,GSM1838795 r1,0:51.00,A:707525221;C:599202602;G:597562199;T:705047589;N:2555171,51,,,,707525221,599202602,597562199,705047589,2555171,SRX1125765,SRS1017742,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.9282,,0.09007,,0.72147,,0.47387,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
39775,SRR2136293,SRX1125764,SRS1017743,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Control 2,GSM1838794,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,Control 2,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,GSM1838794,GSM1838794: Control 2; Danio rerio; RNA Seq,GSM1838794,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838794,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample2_TGACCA.fastq.bz2,fastq,2686989417.0,52686067.0,GSM1838794 r1,0:51,A:728607816;C:615847292;G:614033432;T:725881768;N:2619109,51,,,,728607816,615847292,614033432,725881768,2619109,SRX1125764,SRS1017743,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.92483,,0.09787,,0.7203,,0.45884,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
39776,SRR2136292,SRX1125763,SRS1017744,SRP061855,PRJNA291531,Identification of qkia/c target genes,GSE71573,Transcriptome Analysis,Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.,,pubmed:28867488,,Control 1,GSM1838793,,tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,Control 1,Before mapping  poly N read tails were trimmed  reads ≤40 bases were removed  and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.,trunk,Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80°C until RNA extraction.,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.,Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino,GSM1838793,GSM1838793: Control 1; Danio rerio; RNA Seq,GSM1838793,,1,total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.,GEO Accession:GSM1838793,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP061855,,,Sample1_CGATGT.fastq.bz2,fastq,2920348075.0,57261727.0,GSM1838793 r1,0:51.00,A:788971393;C:671861209;G:669575375;T:787095383;N:2844715,51,,,,788971393,671861209,669575375,787095383,2844715,SRX1125763,SRS1017744,SRA281148,GEO,"Plateforme transcriptome, Biologie, Ecole Normale Supérieure",1,0.92794,,0.09884,,0.71711,,0.4721,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,France,2015-07-30,Pharyngula,Embryo,Trunk,Surface Structure
40162,SRR2937381,SRX1440089,SRS1170438,SRP066406,PRJNA302080,Danio rerio Raw sequence reads,PRJNA302080,Whole Genome Sequencing,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,,,,,T,,strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,T,T,cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx  respectively  by using Trizol regent Invitrogen  USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology  China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers  which was followed by second  strand cDNA synthesis. The double stranded cDNA was further subjected to end repair  phosphorylation  3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp  and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently  the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP066406,,,T.fq.gz,fastq,587807332.0,11996068.0,T,0:49,A:146199755;C:143635765;G:149348442;T:148593898;N:29472,49,,,,146199755,143635765,149348442,148593898,29472,SRX1440089,SRS1170438,SRA312474,National Central University|Chen-Ssu-Ching lab,National Central University,1,0.95023,,0.02672,,0.77889,,0.46839,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2016-11-20,Undetermined,Embryo,Trunk,Surface Structure
40163,SRR2924938,SRX1438257,SRS1168908,SRP066406,PRJNA302080,Danio rerio Raw sequence reads,PRJNA302080,Whole Genome Sequencing,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,,,,,D,,strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,D,D,cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx  respectively  by using Trizol regent Invitrogen  USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology  China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers  which was followed by second  strand cDNA synthesis. The double stranded cDNA was further subjected to end repair  phosphorylation  3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp  and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently  the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP066406,,,D.fq.gz,fastq,535039673.0,10919177.0,D,0:49,A:135797892;C:127799155;G:132966868;T:138440725;N:35033,49,,,,135797892,127799155,132966868,138440725,35033,SRX1438257,SRS1168908,SRA312306,National Central University|Chen-Ssu-Ching lab,National Central University,1,0.93993,,0.0586,,0.73391,,0.46855,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2016-11-19,Undetermined,Embryo,Trunk,Surface Structure
41421,SRR4423115,SRX2245299,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,94 3,94 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0094BC03smallZF.fastq,fastq,697814234.0,14408051.0,maleRID0094BC03smallZF.fastq,0:48.43,A:165337411;C:177790468;G:184204311;T:170482044;N:0,48,,,,165337411,177790468,184204311,170482044,0,SRX2245299,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70426,,0.16215,,0.91027,,0.5459,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41423,SRR4423113,SRX2245297,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Adult male whole body,99 5,99 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0099BC05LargeZF.fastq,fastq,3606425618.0,40350582.0,maleRID0099BC05LargeZF.fastq,0:89.38,A:900873268;C:899774590;G:1079098037;T:726679723;N:0,89,,,,900873268,899774590,1079098037,726679723,0,SRX2245297,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.90069,,0.21287,,0.95726,,0.72186,,53,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41425,SRR4423111,SRX2245295,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,88 3,88 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0088BC03smallZF.fastq,fastq,523776538.0,11118832.0,maleRID0088BC03smallZF.fastq,0:47.11,A:123827431;C:133478804;G:138882662;T:127587641;N:0,47,,,,123827431,133478804,138882662,127587641,0,SRX2245295,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.69556,,0.16368,,0.9093,,0.54838,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41427,SRR4423109,SRX2245293,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,93 3,93 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0093BC03smallZF.fastq,fastq,692750598.0,14286031.0,maleRID0093BC03smallZF.fastq,0:48.49,A:164412063;C:176380331;G:182539801;T:169418403;N:0,48,,,,164412063,176380331,182539801,169418403,0,SRX2245293,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70738,,0.16645,,0.90948,,0.55306,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
48110,SRR7049634,SRX3981085,SRS3205926,SRP141415,PRJNA451191,RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings,PRJNA451191,Other,To identify molecular mechanisms underlying scoliosis spine curvature  we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish  at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown  RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.,,,,,ptk7/+ 11,,isolate:fish #11|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of Danio rerio: scoliosis trunk,ptk7 het 11,ptk7 het 11,Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP141415,,loader:fastq load.py,Ptk7_het_straight_11_R2.fastq.gz Ptk7_het_straight_11_R1.fastq,fastq fastq,10112242392.0,40127946.0,Ptk7 het straight 11 R2.fastq.gz,0:126 1:126,A:2526420409;C:2531445826;G:2613534392;T:2439160326;N:1681439,126,126,,,2526420409,2531445826,2613534392,2439160326,1681439,SRX3981085,SRS3205926,SRA693409,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.83476,0.83453,0.10235,0.10313,0.73614,0.73799,0.46442,0.52808,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,Canada,2018-05-16,Larval,Larval,Trunk,Surface Structure
56303,SRR10916845,SRX7584161,SRS6018089,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 96 hpf,GSM4277146,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277146,GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq,GSM4277146,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277146,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,A2-43_GTCCGC_L002_R1_001.fastq.gz,fastq,2503264497.0,24784797.0,GSM4277146 r1,0:101 1:0,A:610342444;C:605351395;G:584078328;T:703409443;N:82887,101,0,,,610342444,605351395,584078328,703409443,82887,SRX7584161,SRS6018089,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95646,,0.06805,,0.69274,,0.49865,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56304,SRR10916846,SRX7584161,SRS6018089,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 96 hpf,GSM4277146,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277146,GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq,GSM4277146,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277146,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,B3-44_CGATGT_L003_R1_001.fastq.gz,fastq,2225687409.0,22036509.0,GSM4277146 r2,0:101 1:0,A:543949310;C:537645424;G:518948090;T:625038482;N:106103,101,0,,,543949310,537645424,518948090,625038482,106103,SRX7584161,SRS6018089,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.9578,,0.06735,,0.69189,,0.49902,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56305,SRR10916847,SRX7584161,SRS6018089,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 96 hpf,GSM4277146,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277146,GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq,GSM4277146,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277146,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,H3-45_ACTTGA_L003_R1_001.fastq.gz,fastq,2597175105.0,25714605.0,GSM4277146 r3,0:101 1:0,A:634560188;C:628995069;G:615407384;T:718090230;N:122234,101,0,,,634560188,628995069,615407384,718090230,122234,SRX7584161,SRS6018089,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95702,,0.06548,,0.69333,,0.50018,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56306,SRR10916848,SRX7584161,SRS6018089,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 96 hpf,GSM4277146,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277146,GSM4277146: BkF 96 hpf; Danio rerio; RNA Seq,GSM4277146,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277146,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,F3-46_GCCAAT_L003_R1_001.fastq.gz,fastq,2038733480.0,20185480.0,GSM4277146 r4,0:101 1:0,A:496407974;C:493935831;G:480716183;T:567578140;N:95352,101,0,,,496407974,493935831,480716183,567578140,95352,SRX7584161,SRS6018089,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95838,,0.06496,,0.69335,,0.49217,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56307,SRR10916841,SRX7584160,SRS6018088,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 72 hpf,GSM4277145,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277145,GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq,GSM4277145,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277145,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,F1-39_AGTTCC_L001_R1_001.fastq.gz,fastq,2691303671.0,26646571.0,GSM4277145 r1,0:101 1:0,A:665556474;C:642870170;G:620139397;T:761562504;N:1175126,101,0,,,665556474,642870170,620139397,761562504,1175126,SRX7584160,SRS6018088,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95083,,0.06959,,0.68694,,0.49115,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56308,SRR10916842,SRX7584160,SRS6018088,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 72 hpf,GSM4277145,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277145,GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq,GSM4277145,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277145,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,G2-40_ACTGAT_L002_R1_001.fastq.gz,fastq,2579165694.0,25536294.0,GSM4277145 r2,0:101 1:0,A:628949965;C:623927227;G:605984325;T:720216822;N:87355,101,0,,,628949965,623927227,605984325,720216822,87355,SRX7584160,SRS6018088,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95759,,0.06521,,0.6913,,0.49176,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56309,SRR10916843,SRX7584160,SRS6018088,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 72 hpf,GSM4277145,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277145,GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq,GSM4277145,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277145,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,E1-41_AGTCAA_L001_R1_001.fastq.gz,fastq,2601135012.0,25753812.0,GSM4277145 r3,0:101 1:0,A:650835031;C:615158716;G:595000672;T:739001381;N:1139212,101,0,,,650835031,615158716,595000672,739001381,1139212,SRX7584160,SRS6018088,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.94866,,0.07141,,0.68887,,0.48668,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56310,SRR10916844,SRX7584160,SRS6018088,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 72 hpf,GSM4277145,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277145,GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq,GSM4277145,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277145,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,A3-42_ATCACG_L003_R1_001.fastq.gz,fastq,2214733454.0,21928054.0,GSM4277145 r4,0:101 1:0,A:536220771;C:538941586;G:522287992;T:617178828;N:104277,101,0,,,536220771,538941586,522287992,617178828,104277,SRX7584160,SRS6018088,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95924,,0.06516,,0.69061,,0.48876,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56311,SRR10916837,SRX7584159,SRS6018087,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 60 hpf,GSM4277144,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277144,GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq,GSM4277144,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277144,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,G3-35_CAGATC_L003_R1_001.fastq.gz,fastq,2118143821.0,20971721.0,GSM4277144 r1,0:101 1:0,A:519832513;C:509799417;G:496904386;T:591508165;N:99340,101,0,,,519832513,509799417,496904386,591508165,99340,SRX7584159,SRS6018087,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95673,,0.07053,,0.68753,,0.48307,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56312,SRR10916838,SRX7584159,SRS6018087,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 60 hpf,GSM4277144,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277144,GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq,GSM4277144,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277144,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,E4-36_AGTCAA_L004_R1_001.fastq.gz,fastq,2923077966.0,28941366.0,GSM4277144 r2,0:101 1:0,A:716333865;C:709120560;G:684256756;T:813242302;N:124483,101,0,,,716333865,709120560,684256756,813242302,124483,SRX7584159,SRS6018087,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95832,,0.07054,,0.69073,,0.48784,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56313,SRR10916839,SRX7584159,SRS6018087,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 60 hpf,GSM4277144,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277144,GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq,GSM4277144,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277144,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,C2-37_GTGGCC_L002_R1_001.fastq.gz,fastq,2405094012.0,23812812.0,GSM4277144 r3,0:101 1:0,A:595065779;C:573327677;G:550954965;T:685664326;N:81265,101,0,,,595065779,573327677,550954965,685664326,81265,SRX7584159,SRS6018087,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95699,,0.06973,,0.69102,,0.49053,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56314,SRR10916840,SRX7584159,SRS6018087,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 60 hpf,GSM4277144,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277144,GSM4277144: BkF 60 hpf; Danio rerio; RNA Seq,GSM4277144,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277144,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,D3-38_TGACCA_L003_R1_001.fastq.gz,fastq,2347133142.0,23238942.0,GSM4277144 r4,0:101 1:0,A:569276409;C:568869930;G:547564379;T:661311262;N:111162,101,0,,,569276409,568869930,547564379,661311262,111162,SRX7584159,SRS6018087,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95815,,0.06396,,0.69355,,0.48232,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56315,SRR10916833,SRX7584158,SRS6018086,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 48 hpf,GSM4277143,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277143,GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq,GSM4277143,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277143,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,F2-31_GAGTGG_L002_R1_001.fastq.gz,fastq,2619685379.0,25937479.0,GSM4277143 r1,0:101 1:0,A:636766025;C:635045405;G:615398354;T:732386501;N:89094,101,0,,,636766025,635045405,615398354,732386501,89094,SRX7584158,SRS6018086,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95957,,0.06696,,0.69075,,0.47434,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56316,SRR10916834,SRX7584158,SRS6018086,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 48 hpf,GSM4277143,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277143,GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq,GSM4277143,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277143,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,C4-32_GGCTAC_L004_R1_001.fastq.gz,fastq,2896889676.0,28682076.0,GSM4277143 r2,0:101 1:0,A:718661222;C:694075638;G:664012152;T:820018139;N:122525,101,0,,,718661222,694075638,664012152,820018139,122525,SRX7584158,SRS6018086,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95619,,0.07538,,0.6899,,0.47621,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56317,SRR10916835,SRX7584158,SRS6018086,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 48 hpf,GSM4277143,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277143,GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq,GSM4277143,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277143,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,E3-33_ACAGTG_L003_R1_001.fastq.gz,fastq,2334977994.0,23118594.0,GSM4277143 r3,0:101 1:0,A:576482393;C:560480528;G:537818737;T:660085376;N:110960,101,0,,,576482393,560480528,537818737,660085376,110960,SRX7584158,SRS6018086,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95763,,0.06915,,0.69881,,0.47719,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56318,SRR10916836,SRX7584158,SRS6018086,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,BkF 48 hpf,GSM4277143,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,BkF 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:12 μM Benzo[k]fluoranthene,GSM4277143,GSM4277143: BkF 48 hpf; Danio rerio; RNA Seq,GSM4277143,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277143,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,G4-34_ATGTCA_L004_R1_001.fastq.gz,fastq,3090298515.0,30597015.0,GSM4277143 r4,0:101 1:0,A:752311223;C:754003094;G:727487378;T:856366856;N:129964,101,0,,,752311223,754003094,727487378,856366856,129964,SRX7584158,SRS6018086,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.9593,,0.06852,,0.69721,,0.47942,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56319,SRR10916829,SRX7584157,SRS6018085,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 96 hpf,GSM4277142,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO,Control 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:1% DMSO,GSM4277142,GSM4277142: Control 96 hpf; Danio rerio; RNA Seq,GSM4277142,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277142,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,B2-59_GTGAAA_L002_R1_001.fastq.gz,fastq,2458252736.0,24339136.0,GSM4277142 r1,0:101 1:0,A:592844538;C:598120714;G:575281979;T:691922086;N:83419,101,0,,,592844538,598120714,575281979,691922086,83419,SRX7584157,SRS6018085,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95638,,0.06618,,0.69767,,0.46692,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56320,SRR10916830,SRX7584157,SRS6018085,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 96 hpf,GSM4277142,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO,Control 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:1% DMSO,GSM4277142,GSM4277142: Control 96 hpf; Danio rerio; RNA Seq,GSM4277142,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277142,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,D2-60_GTTTCG_L002_R1_001.fastq.gz,fastq,2624445812.0,25984612.0,GSM4277142 r2,0:101 1:0,A:637941230;C:633570363;G:609402380;T:743443765;N:88074,101,0,,,637941230,633570363,609402380,743443765,88074,SRX7584157,SRS6018085,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95491,,0.06814,,0.69455,,0.45801,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56321,SRR10916831,SRX7584157,SRS6018085,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 96 hpf,GSM4277142,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO,Control 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:1% DMSO,GSM4277142,GSM4277142: Control 96 hpf; Danio rerio; RNA Seq,GSM4277142,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277142,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,F4-61_AGTTCC_L004_R1_001.fastq.gz,fastq,2584999050.0,25594050.0,GSM4277142 r3,0:101 1:0,A:630942492;C:629637170;G:606025971;T:718285118;N:108299,101,0,,,630942492,629637170,606025971,718285118,108299,SRX7584157,SRS6018085,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95797,,0.06644,,0.69854,,0.45736,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56322,SRR10916832,SRX7584157,SRS6018085,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 96 hpf,GSM4277142,,tissue:Distal trunk tissue|developmental stage:96 hpf|treatment:1% DMSO,Control 96 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:96 hpf|treatment:1% DMSO,GSM4277142,GSM4277142: Control 96 hpf; Danio rerio; RNA Seq,GSM4277142,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277142,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,B1-62_TAGCTT_L001_R1_001.fastq.gz,fastq,2330595907.0,23075207.0,GSM4277142 r4,0:101 1:0,A:577282093;C:554550745;G:531987957;T:665756273;N:1018839,101,0,,,577282093,554550745,531987957,665756273,1018839,SRX7584157,SRS6018085,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95009,,0.07667,,0.69645,,0.45454,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56323,SRR10916825,SRX7584156,SRS6018083,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 72 hpf,GSM4277141,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO,Control 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:1% DMSO,GSM4277141,GSM4277141: Control 72 hpf; Danio rerio; RNA Seq,GSM4277141,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277141,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,C1-55_GGCTAC_L001_R1_001.fastq.gz,fastq,2503577092.0,24787892.0,GSM4277141 r1,0:101 1:0,A:621449487;C:596176502;G:573313379;T:711542063;N:1095661,101,0,,,621449487,596176502,573313379,711542063,1095661,SRX7584156,SRS6018083,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.94961,,0.07573,,0.69485,,0.45694,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56324,SRR10916826,SRX7584156,SRS6018083,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 72 hpf,GSM4277141,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO,Control 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:1% DMSO,GSM4277141,GSM4277141: Control 72 hpf; Danio rerio; RNA Seq,GSM4277141,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277141,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,A4-56_GATCAG_L004_R1_001.fastq.gz,fastq,2734573586.0,27074986.0,GSM4277141 r2,0:101 1:0,A:672128120;C:674528687;G:630293642;T:757509924;N:113213,101,0,,,672128120,674528687,630293642,757509924,113213,SRX7584156,SRS6018083,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.9596,,0.06704,,0.70218,,0.45451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56325,SRR10916827,SRX7584156,SRS6018083,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 72 hpf,GSM4277141,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO,Control 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:1% DMSO,GSM4277141,GSM4277141: Control 72 hpf; Danio rerio; RNA Seq,GSM4277141,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277141,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,H2-57_ATTCCT_L002_R1_001.fastq.gz,fastq,2875677252.0,28472052.0,GSM4277141 r3,0:101 1:0,A:687980848;C:708003051;G:686913934;T:792682658;N:96761,101,0,,,687980848,708003051,686913934,792682658,96761,SRX7584156,SRS6018083,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95991,,0.06385,,0.69942,,0.46458,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56326,SRR10916828,SRX7584156,SRS6018083,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 72 hpf,GSM4277141,,tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:1% DMSO,Control 72 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:72 hpf|treatment:1% DMSO,GSM4277141,GSM4277141: Control 72 hpf; Danio rerio; RNA Seq,GSM4277141,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277141,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,G1-58_ATGTCA_L001_R1_001.fastq.gz,fastq,2457824799.0,24334899.0,GSM4277141 r4,0:101 1:0,A:586531590;C:602530665;G:582733234;T:684955414;N:1073896,101,0,,,586531590,602530665,582733234,684955414,1073896,SRX7584156,SRS6018083,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95516,,0.06013,,0.70092,,0.45056,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Larval,Larval,Trunk,Surface Structure
56327,SRR10916821,SRX7584155,SRS6018084,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 60 hpf,GSM4277140,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO,Control 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:1% DMSO,GSM4277140,GSM4277140: Control 60 hpf; Danio rerio; RNA Seq,GSM4277140,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277140,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,E2-51_CGTACG_L002_R1_001.fastq.gz,fastq,2631272301.0,26052201.0,GSM4277140 r1,0:101 1:0,A:636992903;C:637434881;G:617397859;T:739358160;N:88498,101,0,,,636992903,637434881,617397859,739358160,88498,SRX7584155,SRS6018084,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95868,,0.06185,,0.69893,,0.45282,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56328,SRR10916822,SRX7584155,SRS6018084,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 60 hpf,GSM4277140,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO,Control 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:1% DMSO,GSM4277140,GSM4277140: Control 60 hpf; Danio rerio; RNA Seq,GSM4277140,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277140,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,H4-52_CCGTCC_L004_R1_001.fastq.gz,fastq,3099842005.0,30691505.0,GSM4277140 r2,0:101 1:0,A:746424596;C:763800562;G:740203116;T:849281933;N:131798,101,0,,,746424596,763800562,740203116,849281933,131798,SRX7584155,SRS6018084,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95949,,0.06262,,0.70283,,0.45043,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56329,SRR10916823,SRX7584155,SRS6018084,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 60 hpf,GSM4277140,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO,Control 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:1% DMSO,GSM4277140,GSM4277140: Control 60 hpf; Danio rerio; RNA Seq,GSM4277140,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277140,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,H1-53_CCGTCC_L001_R1_001.fastq.gz,fastq,2774786534.0,27473134.0,GSM4277140 r3,0:101 1:0,A:660907129;C:687274890;G:662643674;T:762751054;N:1209787,101,0,,,660907129,687274890,662643674,762751054,1209787,SRX7584155,SRS6018084,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95683,,0.05848,,0.70191,,0.45459,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56330,SRR10916824,SRX7584155,SRS6018084,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 60 hpf,GSM4277140,,tissue:Distal trunk tissue|developmental stage:60 hpf|treatment:1% DMSO,Control 60 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:60 hpf|treatment:1% DMSO,GSM4277140,GSM4277140: Control 60 hpf; Danio rerio; RNA Seq,GSM4277140,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277140,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,B4-54_TAGCTT_L004_R1_001.fastq.gz,fastq,2960262530.0,29309530.0,GSM4277140 r4,0:101 1:0,A:740908620;C:699500257;G:674362882;T:845364000;N:126771,101,0,,,740908620,699500257,674362882,845364000,126771,SRX7584155,SRS6018084,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95529,,0.07342,,0.69783,,0.45292,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56331,SRR10916817,SRX7584154,SRS6018082,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 48 hpf,GSM4277139,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO,Control 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:1% DMSO,GSM4277139,GSM4277139: Control 48 hpf; Danio rerio; RNA Seq,GSM4277139,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277139,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,D4-47_CTTGTA_L004_R1_001.fastq.gz,fastq,2845394927.0,28172227.0,GSM4277139 r1,0:101 1:0,A:696407866;C:689539633;G:660246907;T:799078393;N:122128,101,0,,,696407866,689539633,660246907,799078393,122128,SRX7584154,SRS6018082,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95735,,0.07029,,0.70094,,0.41347,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56332,SRR10916818,SRX7584154,SRS6018082,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 48 hpf,GSM4277139,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO,Control 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:1% DMSO,GSM4277139,GSM4277139: Control 48 hpf; Danio rerio; RNA Seq,GSM4277139,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277139,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,D1-48_CTTGTA_L001_R1_001.fastq.gz,fastq,2492562638.0,24678838.0,GSM4277139 r2,0:101 1:0,A:614317033;C:596890437;G:569548715;T:710717116;N:1089337,101,0,,,614317033,596890437,569548715,710717116,1089337,SRX7584154,SRS6018082,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95109,,0.06997,,0.69635,,0.459,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56333,SRR10916819,SRX7584154,SRS6018082,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 48 hpf,GSM4277139,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO,Control 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:1% DMSO,GSM4277139,GSM4277139: Control 48 hpf; Danio rerio; RNA Seq,GSM4277139,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277139,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,C3-49_TTAGGC_L003_R1_001.fastq.gz,fastq,2323634684.0,23006284.0,GSM4277139 r3,0:101 1:0,A:560892305;C:565585370;G:543493908;T:653554844;N:108257,101,0,,,560892305,565585370,543493908,653554844,108257,SRX7584154,SRS6018082,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.96012,,0.0605,,0.70891,,0.44674,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
56334,SRR10916820,SRX7584154,SRS6018082,SRP243451,PRJNA602305,Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.,GSE143945,Transcriptome Analysis,Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 µM BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 µM benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.,,pubmed:32384158,,Control 48 hpf,GSM4277139,,tissue:Distal trunk tissue|developmental stage:48 hpf|treatment:1% DMSO,Control 48 hpf,Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.,Distal trunk tissue,Static chemical exposures 1% DMSO or 12 μM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5˚C.,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.,developmental stage:48 hpf|treatment:1% DMSO,GSM4277139,GSM4277139: Control 48 hpf; Danio rerio; RNA Seq,GSM4277139,,1,Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.,GEO Accession:GSM4277139,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP243451,,,A1-50_GATCAG_L001_R1_001.fastq.gz,fastq,2247754394.0,22254994.0,GSM4277139 r4,0:101 1:0,A:566228379;C:548437322;G:509638046;T:622507773;N:942874,101,0,,,566228379,548437322,509638046,622507773,942874,SRX7584154,SRS6018082,SRA1028878,GEO,"Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University",1,0.95297,,0.06518,,0.71039,,0.44188,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-01-20,Hatching,Embryo,Trunk,Surface Structure
57280,SRR11302641,SRX7908670,SRS6316242,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D22,GSM4410633,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D22,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410633,GSM4410633: zebrafish 990s D22; Danio rerio; RNA Seq,GSM4410633,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410633,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D22.bam,bam,14952235.0,302958.0,GSM4410633 r1,0:49.35,A:3811307;C:3645371;G:3617661;T:3873396;N:4500,49,,,,3811307,3645371,3617661,3873396,4500,SRX7908670,SRS6316242,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96635,,0.06324,,0.87769,,0.49502,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57281,SRR11302640,SRX7908669,SRS6316243,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D21,GSM4410632,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D21,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410632,GSM4410632: zebrafish 990s D21; Danio rerio; RNA Seq,GSM4410632,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410632,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D21.bam,bam,12301286.0,248613.0,GSM4410632 r1,0:49.48,A:3216338;C:2918960;G:2899913;T:3262285;N:3790,49,,,,3216338,2918960,2899913,3262285,3790,SRX7908669,SRS6316243,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96446,,0.11117,,0.9137,,0.51287,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57282,SRR11302639,SRX7908668,SRS6316241,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D20,GSM4410631,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D20,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410631,GSM4410631: zebrafish 990s D20; Danio rerio; RNA Seq,GSM4410631,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410631,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D20.bam,bam,13841010.0,280169.0,GSM4410631 r1,0:49.40,A:3567280;C:3336013;G:3310051;T:3623298;N:4368,49,,,,3567280,3336013,3310051,3623298,4368,SRX7908668,SRS6316241,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96393,,0.08232,,0.92616,,0.49002,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57283,SRR11302638,SRX7908667,SRS6316240,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D2,GSM4410630,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D2,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410630,GSM4410630: zebrafish 990s D2; Danio rerio; RNA Seq,GSM4410630,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410630,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D2.bam,bam,13249032.0,267250.0,GSM4410630 r1,0:49.58,A:3526925;C:3081325;G:3060212;T:3576643;N:3927,49,,,,3526925,3081325,3060212,3576643,3927,SRX7908667,SRS6316240,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95057,,0.1848,,0.92504,,0.48003,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57284,SRR11302637,SRX7908666,SRS6316237,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D19,GSM4410629,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D19,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410629,GSM4410629: zebrafish 990s D19; Danio rerio; RNA Seq,GSM4410629,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410629,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D19.bam,bam,24639240.0,496686.0,GSM4410629 r1,0:49.61,A:6408578;C:5886841;G:5845099;T:6491229;N:7493,49,,,,6408578,5886841,5845099,6491229,7493,SRX7908666,SRS6316237,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96339,,0.06751,,0.91198,,0.46563,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57285,SRR11302636,SRX7908665,SRS6316236,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D18,GSM4410628,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D18,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410628,GSM4410628: zebrafish 990s D18; Danio rerio; RNA Seq,GSM4410628,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410628,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D18.bam,bam,6244321.0,125915.0,GSM4410628 r1,0:49.59,A:1600346;C:1515162;G:1505658;T:1621317;N:1838,49,,,,1600346,1515162,1505658,1621317,1838,SRX7908665,SRS6316236,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96639,,0.09462,,0.93275,,0.51899,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57286,SRR11302635,SRX7908664,SRS6316239,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D17,GSM4410627,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D17,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410627,GSM4410627: zebrafish 990s D17; Danio rerio; RNA Seq,GSM4410627,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410627,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D17.bam,bam,19546818.0,394040.0,GSM4410627 r1,0:49.61,A:5084961;C:4673304;G:4637984;T:5144779;N:5790,49,,,,5084961,4673304,4637984,5144779,5790,SRX7908664,SRS6316239,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96388,,0.09619,,0.92419,,0.46267,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57287,SRR11302634,SRX7908663,SRS6316238,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D16,GSM4410626,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D16,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410626,GSM4410626: zebrafish 990s D16; Danio rerio; RNA Seq,GSM4410626,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410626,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D16.bam,bam,35129013.0,708869.0,GSM4410626 r1,0:49.56,A:9128792;C:8378350;G:8324629;T:9287068;N:10174,49,,,,9128792,8378350,8324629,9287068,10174,SRX7908663,SRS6316238,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96185,,0.07724,,0.91597,,0.48886,,41,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57288,SRR11302633,SRX7908662,SRS6316235,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D15,GSM4410625,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D15,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410625,GSM4410625: zebrafish 990s D15; Danio rerio; RNA Seq,GSM4410625,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410625,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D15.bam,bam,20555028.0,414281.0,GSM4410625 r1,0:49.62,A:5268027;C:4987353;G:4954575;T:5338793;N:6280,49,,,,5268027,4987353,4954575,5338793,6280,SRX7908662,SRS6316235,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96672,,0.07072,,0.92295,,0.48391,,44,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57289,SRR11302632,SRX7908661,SRS6316234,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D14,GSM4410624,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D14,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410624,GSM4410624: zebrafish 990s D14; Danio rerio; RNA Seq,GSM4410624,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410624,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D14.bam,bam,25155383.0,507445.0,GSM4410624 r1,0:49.57,A:6589687;C:5956715;G:5911932;T:6689599;N:7450,49,,,,6589687,5956715,5911932,6689599,7450,SRX7908661,SRS6316234,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9592,,0.1259,,0.91175,,0.47661,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57290,SRR11302631,SRX7908660,SRS6316232,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D13,GSM4410623,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D13,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410623,GSM4410623: zebrafish 990s D13; Danio rerio; RNA Seq,GSM4410623,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410623,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D13.bam,bam,26252350.0,529709.0,GSM4410623 r1,0:49.56,A:6824395;C:6273054;G:6234203;T:6912870;N:7828,49,,,,6824395,6273054,6234203,6912870,7828,SRX7908660,SRS6316232,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96307,,0.10084,,0.90445,,0.47847,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57291,SRR11302630,SRX7908659,SRS6316233,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D12,GSM4410622,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D12,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410622,GSM4410622: zebrafish 990s D12; Danio rerio; RNA Seq,GSM4410622,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410622,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D12.bam,bam,26274219.0,529278.0,GSM4410622 r1,0:49.64,A:6795815;C:6306706;G:6259822;T:6904582;N:7294,49,,,,6795815,6306706,6259822,6904582,7294,SRX7908659,SRS6316233,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95859,,0.10058,,0.90106,,0.46651,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57292,SRR11302629,SRX7908658,SRS6316231,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D11,GSM4410621,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D11,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410621,GSM4410621: zebrafish 990s D11; Danio rerio; RNA Seq,GSM4410621,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410621,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D11.bam,bam,10464062.0,211250.0,GSM4410621 r1,0:49.53,A:2687251;C:2533437;G:2512865;T:2727443;N:3066,49,,,,2687251,2533437,2512865,2727443,3066,SRX7908658,SRS6316231,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96414,,0.06516,,0.94255,,0.53005,,45,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57293,SRR11302628,SRX7908657,SRS6316229,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D10,GSM4410620,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D10,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410620,GSM4410620: zebrafish 990s D10; Danio rerio; RNA Seq,GSM4410620,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410620,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D10.bam,bam,22770979.0,459186.0,GSM4410620 r1,0:49.59,A:5826113;C:5533708;G:5495964;T:5908461;N:6733,49,,,,5826113,5533708,5495964,5908461,6733,SRX7908657,SRS6316229,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96785,,0.06209,,0.90784,,0.48004,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57294,SRR11302627,SRX7908656,SRS6316230,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s D1,GSM4410619,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s D1,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410619,GSM4410619: zebrafish 990s D1; Danio rerio; RNA Seq,GSM4410619,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410619,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_D1.bam,bam,25924183.0,521171.0,GSM4410619 r1,0:49.74,A:6729937;C:6200705;G:6153858;T:6832585;N:7098,49,,,,6729937,6200705,6153858,6832585,7098,SRX7908656,SRS6316230,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96292,,0.10401,,0.89721,,0.48829,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57295,SRR11302626,SRX7908655,SRS6316227,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C9,GSM4410618,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C9,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410618,GSM4410618: zebrafish 990s C9; Danio rerio; RNA Seq,GSM4410618,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410618,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C9.bam,bam,24266046.0,489282.0,GSM4410618 r1,0:49.60,A:6303157;C:5796448;G:5758377;T:6400971;N:7093,49,,,,6303157,5796448,5758377,6400971,7093,SRX7908655,SRS6316227,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96377,,0.09952,,0.93604,,0.47909,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57296,SRR11302625,SRX7908654,SRS6316228,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C8,GSM4410617,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C8,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410617,GSM4410617: zebrafish 990s C8; Danio rerio; RNA Seq,GSM4410617,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410617,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C8.bam,bam,21899008.0,441712.0,GSM4410617 r1,0:49.58,A:5747348;C:5177667;G:5136928;T:5830424;N:6641,49,,,,5747348,5177667,5136928,5830424,6641,SRX7908654,SRS6316228,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95958,,0.13065,,0.92216,,0.46914,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57297,SRR11302624,SRX7908653,SRS6316226,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C7,GSM4410616,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C7,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410616,GSM4410616: zebrafish 990s C7; Danio rerio; RNA Seq,GSM4410616,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410616,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C7.bam,bam,28404846.0,573859.0,GSM4410616 r1,0:49.50,A:7235244;C:6926753;G:6877946;T:7356336;N:8567,49,,,,7235244,6926753,6877946,7356336,8567,SRX7908653,SRS6316226,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96435,,0.06783,,0.91492,,0.48294,,42,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57298,SRR11302623,SRX7908652,SRS6316224,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C6,GSM4410615,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C6,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410615,GSM4410615: zebrafish 990s C6; Danio rerio; RNA Seq,GSM4410615,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410615,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C6.bam,bam,18860719.0,381549.0,GSM4410615 r1,0:49.43,A:5074635;C:4333167;G:4301649;T:5145437;N:5831,49,,,,5074635,4333167,4301649,5145437,5831,SRX7908652,SRS6316224,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95523,,0.16234,,0.90329,,0.47409,,41,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57299,SRR11302622,SRX7908651,SRS6316225,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C5,GSM4410614,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C5,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410614,GSM4410614: zebrafish 990s C5; Danio rerio; RNA Seq,GSM4410614,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410614,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C5.bam,bam,15089981.0,304859.0,GSM4410614 r1,0:49.50,A:3951385;C:3573935;G:3555893;T:4003894;N:4874,49,,,,3951385,3573935,3555893,4003894,4874,SRX7908651,SRS6316225,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96352,,0.17134,,0.93265,,0.47004,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57300,SRR11302621,SRX7908650,SRS6316222,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C4,GSM4410613,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C4,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410613,GSM4410613: zebrafish 990s C4; Danio rerio; RNA Seq,GSM4410613,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410613,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C4.bam,bam,19269405.0,388669.0,GSM4410613 r1,0:49.58,A:5084174;C:4527015;G:4489207;T:5163246;N:5763,49,,,,5084174,4527015,4489207,5163246,5763,SRX7908650,SRS6316222,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95519,,0.12584,,0.91977,,0.48712,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57301,SRR11302620,SRX7908649,SRS6316223,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C3,GSM4410612,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C3,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410612,GSM4410612: zebrafish 990s C3; Danio rerio; RNA Seq,GSM4410612,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410612,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C3.bam,bam,26296146.0,529798.0,GSM4410612 r1,0:49.63,A:6879183;C:6235952;G:6187938;T:6985257;N:7816,49,,,,6879183,6235952,6187938,6985257,7816,SRX7908649,SRS6316223,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9614,,0.13063,,0.92693,,0.48691,,44,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57302,SRR11302619,SRX7908648,SRS6316221,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C24,GSM4410611,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C24,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410611,GSM4410611: zebrafish 990s C24; Danio rerio; RNA Seq,GSM4410611,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410611,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C24.bam,bam,20420608.0,411528.0,GSM4410611 r1,0:49.62,A:5331504;C:4853719;G:4820428;T:5408957;N:6000,49,,,,5331504,4853719,4820428,5408957,6000,SRX7908648,SRS6316221,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96386,,0.11067,,0.93474,,0.44648,,42,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57303,SRR11302618,SRX7908647,SRS6316219,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C23,GSM4410610,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C23,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410610,GSM4410610: zebrafish 990s C23; Danio rerio; RNA Seq,GSM4410610,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410610,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C23.bam,bam,35047445.0,705646.0,GSM4410610 r1,0:49.67,A:9165559;C:8316903;G:8242039;T:9312819;N:10125,49,,,,9165559,8316903,8242039,9312819,10125,SRX7908647,SRS6316219,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95667,,0.08618,,0.90662,,0.48076,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57304,SRR11302617,SRX7908646,SRS6316220,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C22,GSM4410609,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C22,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410609,GSM4410609: zebrafish 990s C22; Danio rerio; RNA Seq,GSM4410609,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410609,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C22.bam,bam,26040133.0,524602.0,GSM4410609 r1,0:49.64,A:6788556;C:6199193;G:6157557;T:6887011;N:7816,49,,,,6788556,6199193,6157557,6887011,7816,SRX7908646,SRS6316220,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95869,,0.11718,,0.9027,,0.4912,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57305,SRR11302616,SRX7908645,SRS6316217,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C21,GSM4410608,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C21,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410608,GSM4410608: zebrafish 990s C21; Danio rerio; RNA Seq,GSM4410608,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410608,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C21.bam,bam,27771299.0,564142.0,GSM4410608 r1,0:49.23,A:7277456;C:6567924;G:6520282;T:7397263;N:8374,49,,,,7277456,6567924,6520282,7397263,8374,SRX7908645,SRS6316217,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96216,,0.08311,,0.92214,,0.484,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57306,SRR11302615,SRX7908644,SRS6316218,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C20,GSM4410607,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C20,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410607,GSM4410607: zebrafish 990s C20; Danio rerio; RNA Seq,GSM4410607,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410607,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C20.bam,bam,12727564.0,257166.0,GSM4410607 r1,0:49.49,A:3253378;C:3091074;G:3068783;T:3310426;N:3903,49,,,,3253378,3091074,3068783,3310426,3903,SRX7908644,SRS6316218,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96581,,0.09966,,0.92336,,0.46559,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57307,SRR11302614,SRX7908643,SRS6316216,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C2,GSM4410606,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C2,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410606,GSM4410606: zebrafish 990s C2; Danio rerio; RNA Seq,GSM4410606,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410606,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C2.bam,bam,24641347.0,496145.0,GSM4410606 r1,0:49.67,A:6362402;C:5928362;G:5889128;T:6454430;N:7025,49,,,,6362402,5928362,5889128,6454430,7025,SRX7908643,SRS6316216,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96422,,0.09577,,0.9095,,0.47689,,41,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57308,SRR11302613,SRX7908642,SRS6316215,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C19,GSM4410605,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C19,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410605,GSM4410605: zebrafish 990s C19; Danio rerio; RNA Seq,GSM4410605,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410605,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C19.bam,bam,35386657.0,712451.0,GSM4410605 r1,0:49.67,A:9180689;C:8467349;G:8402491;T:9325656;N:10472,49,,,,9180689,8467349,8402491,9325656,10472,SRX7908642,SRS6316215,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96283,,0.1015,,0.87852,,0.47362,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57309,SRR11302612,SRX7908641,SRS6316214,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C18,GSM4410604,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C18,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410604,GSM4410604: zebrafish 990s C18; Danio rerio; RNA Seq,GSM4410604,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410604,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C18.bam,bam,17769590.0,358461.0,GSM4410604 r1,0:49.57,A:4590943;C:4269740;G:4239656;T:4663920;N:5331,49,,,,4590943,4269740,4239656,4663920,5331,SRX7908641,SRS6316214,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9647,,0.09031,,0.93288,,0.48597,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57310,SRR11302611,SRX7908640,SRS6316213,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C17,GSM4410603,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C17,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410603,GSM4410603: zebrafish 990s C17; Danio rerio; RNA Seq,GSM4410603,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410603,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C17.bam,bam,32426584.0,653000.0,GSM4410603 r1,0:49.66,A:8461669;C:7712485;G:7651317;T:8591564;N:9549,49,,,,8461669,7712485,7651317,8591564,9549,SRX7908640,SRS6316213,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9592,,0.08874,,0.91259,,0.49461,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57311,SRR11302610,SRX7908639,SRS6316212,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C16,GSM4410602,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C16,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410602,GSM4410602: zebrafish 990s C16; Danio rerio; RNA Seq,GSM4410602,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410602,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C16.bam,bam,25635088.0,516511.0,GSM4410602 r1,0:49.63,A:6592405;C:6192402;G:6144035;T:6698710;N:7536,49,,,,6592405,6192402,6144035,6698710,7536,SRX7908639,SRS6316212,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96488,,0.06936,,0.90636,,0.48394,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57312,SRR11302609,SRX7908638,SRS6316211,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C15,GSM4410601,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C15,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410601,GSM4410601: zebrafish 990s C15; Danio rerio; RNA Seq,GSM4410601,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410601,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C15.bam,bam,24612894.0,495477.0,GSM4410601 r1,0:49.68,A:6387972;C:5887843;G:5848486;T:6481347;N:7246,49,,,,6387972,5887843,5848486,6481347,7246,SRX7908638,SRS6316211,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96143,,0.11709,,0.91139,,0.48454,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57313,SRR11302608,SRX7908637,SRS6316210,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C14,GSM4410600,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C14,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410600,GSM4410600: zebrafish 990s C14; Danio rerio; RNA Seq,GSM4410600,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410600,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C14.bam,bam,23180351.0,466251.0,GSM4410600 r1,0:49.72,A:6010197;C:5556779;G:5513064;T:6093732;N:6579,49,,,,6010197,5556779,5513064,6093732,6579,SRX7908637,SRS6316210,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96353,,0.10838,,0.91863,,0.4849,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57314,SRR11302607,SRX7908636,SRS6316209,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C13,GSM4410599,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C13,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410599,GSM4410599: zebrafish 990s C13; Danio rerio; RNA Seq,GSM4410599,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410599,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C13.bam,bam,29064624.0,585464.0,GSM4410599 r1,0:49.64,A:7486030;C:7009056;G:6957087;T:7604008;N:8443,49,,,,7486030,7009056,6957087,7604008,8443,SRX7908636,SRS6316209,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96286,,0.10457,,0.92805,,0.47785,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57315,SRR11302606,SRX7908635,SRS6316208,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C12,GSM4410598,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C12,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410598,GSM4410598: zebrafish 990s C12; Danio rerio; RNA Seq,GSM4410598,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410598,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C12.bam,bam,24139133.0,486052.0,GSM4410598 r1,0:49.66,A:6234424;C:5812036;G:5765520;T:6319939;N:7214,49,,,,6234424,5812036,5765520,6319939,7214,SRX7908635,SRS6316208,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96519,,0.07726,,0.90713,,0.4802,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57316,SRR11302605,SRX7908634,SRS6316207,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C11,GSM4410597,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C11,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410597,GSM4410597: zebrafish 990s C11; Danio rerio; RNA Seq,GSM4410597,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410597,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C11.bam,bam,16322856.0,329244.0,GSM4410597 r1,0:49.58,A:4485023;C:3646315;G:3622640;T:4563901;N:4977,49,,,,4485023,3646315,3622640,4563901,4977,SRX7908634,SRS6316207,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.94782,,0.31171,,0.93539,,0.48256,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57317,SRR11302604,SRX7908633,SRS6316205,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C10,GSM4410596,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C10,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410596,GSM4410596: zebrafish 990s C10; Danio rerio; RNA Seq,GSM4410596,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410596,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C10.bam,bam,21009208.0,423572.0,GSM4410596 r1,0:49.60,A:5465149;C:5010550;G:4980276;T:5546702;N:6531,49,,,,5465149,5010550,4980276,5546702,6531,SRX7908633,SRS6316205,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96405,,0.10732,,0.92744,,0.48269,,39,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57318,SRR11302603,SRX7908632,SRS6316206,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s C1,GSM4410595,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s C1,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410595,GSM4410595: zebrafish 990s C1; Danio rerio; RNA Seq,GSM4410595,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410595,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_C1.bam,bam,26901512.0,541337.0,GSM4410595 r1,0:49.69,A:6970707;C:6446413;G:6411599;T:7064656;N:8137,49,,,,6970707,6446413,6411599,7064656,8137,SRX7908632,SRS6316206,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9641,,0.09528,,0.92346,,0.50558,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57319,SRR11302602,SRX7908631,SRS6316202,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B9,GSM4410594,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B9,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410594,GSM4410594: zebrafish 990s B9; Danio rerio; RNA Seq,GSM4410594,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410594,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B9.bam,bam,15426612.0,310884.0,GSM4410594 r1,0:49.62,A:4080022;C:3616468;G:3595348;T:4130253;N:4521,49,,,,4080022,3616468,3595348,4130253,4521,SRX7908631,SRS6316202,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95866,,0.18239,,0.93306,,0.49468,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57320,SRR11302601,SRX7908630,SRS6316204,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B8,GSM4410593,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B8,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410593,GSM4410593: zebrafish 990s B8; Danio rerio; RNA Seq,GSM4410593,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410593,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B8.bam,bam,16209285.0,326585.0,GSM4410593 r1,0:49.63,A:4198717;C:3887458;G:3856999;T:4261238;N:4873,49,,,,4198717,3887458,3856999,4261238,4873,SRX7908630,SRS6316204,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.95752,,0.11124,,0.93876,,0.48231,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57321,SRR11302600,SRX7908629,SRS6316200,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B7,GSM4410592,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B7,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410592,GSM4410592: zebrafish 990s B7; Danio rerio; RNA Seq,GSM4410592,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410592,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B7.bam,bam,13053261.0,262841.0,GSM4410592 r1,0:49.66,A:3407078;C:3104309;G:3085740;T:3452172;N:3962,49,,,,3407078,3104309,3085740,3452172,3962,SRX7908629,SRS6316200,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.9621,,0.14005,,0.94339,,0.48716,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57322,SRR11302599,SRX7908628,SRS6316203,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B6,GSM4410591,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B6,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410591,GSM4410591: zebrafish 990s B6; Danio rerio; RNA Seq,GSM4410591,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410591,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B6.bam,bam,18688513.0,377150.0,GSM4410591 r1,0:49.55,A:4811790;C:4506958;G:4476764;T:4887270;N:5731,49,,,,4811790,4506958,4476764,4887270,5731,SRX7908628,SRS6316203,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96323,,0.09461,,0.91492,,0.4842,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57323,SRR11302598,SRX7908627,SRS6316201,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B5,GSM4410590,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B5,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410590,GSM4410590: zebrafish 990s B5; Danio rerio; RNA Seq,GSM4410590,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410590,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B5.bam,bam,23305863.0,469800.0,GSM4410590 r1,0:49.61,A:5996295;C:5637264;G:5603679;T:6061625;N:7000,49,,,,5996295,5637264,5603679,6061625,7000,SRX7908627,SRS6316201,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96423,,0.07727,,0.91581,,0.46864,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57324,SRR11302597,SRX7908626,SRS6316197,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B4,GSM4410589,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B4,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410589,GSM4410589: zebrafish 990s B4; Danio rerio; RNA Seq,GSM4410589,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410589,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B4.bam,bam,14198609.0,286330.0,GSM4410589 r1,0:49.59,A:3685085;C:3392571;G:3377981;T:3738614;N:4358,49,,,,3685085,3392571,3377981,3738614,4358,SRX7908626,SRS6316197,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96687,,0.12743,,0.94134,,0.50108,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57325,SRR11302596,SRX7908625,SRS6316199,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B3,GSM4410588,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B3,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410588,GSM4410588: zebrafish 990s B3; Danio rerio; RNA Seq,GSM4410588,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410588,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B3.bam,bam,21337200.0,430023.0,GSM4410588 r1,0:49.62,A:5500444;C:5141927;G:5111797;T:5576378;N:6654,49,,,,5500444,5141927,5111797,5576378,6654,SRX7908625,SRS6316199,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96416,,0.07969,,0.90218,,0.47964,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57326,SRR11302595,SRX7908624,SRS6316198,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B24,GSM4410587,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B24,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410587,GSM4410587: zebrafish 990s B24; Danio rerio; RNA Seq,GSM4410587,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410587,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B24.bam,bam,14884174.0,300927.0,GSM4410587 r1,0:49.46,A:3847326;C:3570345;G:3546698;T:3915410;N:4395,49,,,,3847326,3570345,3546698,3915410,4395,SRX7908624,SRS6316198,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96401,,0.10549,,0.9389,,0.47099,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57327,SRR11302594,SRX7908623,SRS6316195,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B23,GSM4410586,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B23,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410586,GSM4410586: zebrafish 990s B23; Danio rerio; RNA Seq,GSM4410586,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410586,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B23.bam,bam,21727602.0,437959.0,GSM4410586 r1,0:49.61,A:5617471;C:5219687;G:5183659;T:5700225;N:6560,49,,,,5617471,5219687,5183659,5700225,6560,SRX7908623,SRS6316195,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96243,,0.06801,,0.877,,0.50398,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57328,SRR11302593,SRX7908622,SRS6316196,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B22,GSM4410585,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B22,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410585,GSM4410585: zebrafish 990s B22; Danio rerio; RNA Seq,GSM4410585,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410585,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B22.bam,bam,14808460.0,298872.0,GSM4410585 r1,0:49.55,A:3814070;C:3570992;G:3546502;T:3872564;N:4332,49,,,,3814070,3570992,3546502,3872564,4332,SRX7908622,SRS6316196,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96236,,0.09761,,0.93908,,0.47544,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57329,SRR11302592,SRX7908621,SRS6316192,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B21,GSM4410584,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B21,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410584,GSM4410584: zebrafish 990s B21; Danio rerio; RNA Seq,GSM4410584,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410584,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B21.bam,bam,7756712.0,157032.0,GSM4410584 r1,0:49.40,A:2049070;C:1821395;G:1808619;T:2075260;N:2368,49,,,,2049070,1821395,1808619,2075260,2368,SRX7908621,SRS6316192,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96154,,0.21386,,0.9403,,0.52429,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure
57330,SRR11302591,SRX7908620,SRS6316194,SRP252691,PRJNA612443,Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis,GSE146923,Transcriptome Analysis,Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space  and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing,,pubmed:32483144,,zebrafish 990s B20,GSM4410583,,source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,zebrafish 990s B20,bcl2fastq   demultiplexing sequenced reads were trimmed for adaptor sequence  and then mapped to the zebrafish reference genome danRer11 using TapHat2  Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis  all raw counts from all cells of each of the three sample plates plate 123  plate 989  plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto  SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples,zebrafish,,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,,tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf,GSM4410583,GSM4410583: zebrafish 990s B20; Danio rerio; RNA Seq,GSM4410583,,1,FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol,GEO Accession:GSM4410583,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP252691,,intentional duplicate|dangling references:treat as unmapped,zebrafish_990s_B20.bam,bam,16812241.0,340050.0,GSM4410583 r1,0:49.44,A:4301130;C:4085399;G:4056346;T:4364188;N:5178,49,,,,4301130,4085399,4056346,4364188,5178,SRX7908620,SRS6316194,SRA1054549,GEO,"Betsholtz, ICMC - MedH, Karolinska Institutet",1,0.96716,,0.06463,,0.91956,,0.48441,,46,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2020-03-13,Hatching,Embryo,Trunk,Surface Structure