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
40970,SRR3498280,SRX1756826,SRS1433357,SRP074847,PRJNA321312,mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81335,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,48hpf E1,GSM2150744,,source name:Endothelial cell|developmental stage:48 hpf|tissue:Endothelial|stain:GFP,48hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .,Endothelial cell,,Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48 hpf|tissue:Endothelial|stain:GFP,GSM2150744,GSM2150744: 48hpf E1; Danio rerio; RNA Seq,GSM2150744,,1,Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150744,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074847,,,EF_034_002_CGATGT_L002_R1.fastq.gz,fastq,485202316.0,6384241.0,GSM2150744 r1,0:76,A:128473144;C:107489507;G:107138177;T:135707012;N:6394476,76,,,,128473144,107489507,107138177,135707012,6394476,SRX1756826,SRS1433357,SRA424807,GEO,"Internal Medicine, Yale University",1,0.89084,,0.1385,,0.71985,,0.4908,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40975,SRR3498291,SRX1756837,SRS1433368,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 48hpf E2,GSM2150816,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,NoEndo 48hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150816,GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq,GSM2150816,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150816,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_48hpf_E2.fastq.gz,fastq,553364740.0,7281115.0,GSM2150816 r1,0:76,A:129173344;C:134804122;G:141026546;T:148331467;N:29261,76,,,,129173344,134804122,141026546,148331467,29261,SRX1756837,SRS1433368,SRA424808,GEO,"Internal Medicine, Yale University",1,1e-05,,0.0,,0.99997,,0.0,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40976,SRR3498290,SRX1756836,SRS1433367,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,NoEndo 48hpf E1,GSM2150815,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,NoEndo 48hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150815,GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq,GSM2150815,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150815,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,NoEndo_48hpf_E1.fastq.gz,fastq,1204752152.0,15852002.0,GSM2150815 r1,0:76,A:297517299;C:293969730;G:317491224;T:295696492;N:77407,76,,,,297517299,293969730,317491224,295696492,77407,SRX1756836,SRS1433367,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40981,SRR3498285,SRX1756831,SRS1433362,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 48hpf E2,GSM2150810,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,Endo 48hpf E2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150810,GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq,GSM2150810,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150810,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_48hpf_E2.fastq.gz,fastq,1254556624.0,16507324.0,GSM2150810 r1,0:76,A:316229540;C:323340793;G:307552357;T:307354555;N:79379,76,,,,316229540,323340793,307552357,307354555,79379,SRX1756831,SRS1433362,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
40982,SRR3498284,SRX1756830,SRS1433361,SRP074848,PRJNA321321,microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues,GSE81340,Transcriptome Analysis,Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate,parent bioproject:PRJNA321317,pubmed:28350988;pubmed:33273096,,Endo 48hpf E1,GSM2150809,,source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP,Endo 48hpf E1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,Endothelial cell,,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.,developmental stage:48hpf|tissue:Endothelial|stain:GFP,GSM2150809,GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq,GSM2150809,,1,Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2150809,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,,SRP074848,,,Endo_48hpf_E1.fastq.gz,fastq,1449497080.0,19072330.0,GSM2150809 r1,0:76,A:362564557;C:370330864;G:364749441;T:351760774;N:91444,76,,,,362564557,370330864,364749441,351760774,91444,SRX1756830,SRS1433361,SRA424808,GEO,"Internal Medicine, Yale University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,United States,2016-05-11,Hatching,Embryo,Endothelium,Cardiovascular System
42141,SRR5443688,SRX2733020,SRS2120917,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 3,GSM2574373,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574373,GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq,GSM2574373,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M3_S6_L001_R1_001.fastq.gz,fastq,1290470348.0,17096427.0,GSM2574373 r1,0:75.48 1:0,A:320847705;C:319435806;G:300073193;T:350044923;N:68721,75,0,,,320847705,319435806,300073193,350044923,68721,SRX2733020,SRS2120917,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.94339,,0.05762,,0.72232,,0.50799,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42142,SRR5443689,SRX2733020,SRS2120917,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 3,GSM2574373,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574373,GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq,GSM2574373,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M3_S6_L002_R1_001.fastq.gz,fastq,1274417413.0,16883601.0,GSM2574373 r2,0:75.48 1:0,A:316659737;C:315517172;G:296527344;T:345645123;N:68037,75,0,,,316659737,315517172,296527344,345645123,68037,SRX2733020,SRS2120917,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.94193,,0.05753,,0.7236,,0.50991,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42143,SRR5443690,SRX2733020,SRS2120917,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 3,GSM2574373,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574373,GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq,GSM2574373,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M3_S6_L003_R1_001.fastq.gz,fastq,1267650302.0,16794051.0,GSM2574373 r3,0:75.48 1:0,A:316851687;C:313922763;G:294562163;T:342271337;N:42352,75,0,,,316851687,313922763,294562163,342271337,42352,SRX2733020,SRS2120917,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93935,,0.05711,,0.72421,,0.51344,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42144,SRR5443691,SRX2733020,SRS2120917,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 3,GSM2574373,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574373,GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq,GSM2574373,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M3_S6_L004_R1_001.fastq.gz,fastq,1272371755.0,16856553.0,GSM2574373 r4,0:75.48 1:0,A:317627046;C:315030569;G:295859300;T:343808592;N:46248,75,0,,,317627046,315030569,295859300,343808592,46248,SRX2733020,SRS2120917,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.94038,,0.05657,,0.72391,,0.5115,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42145,SRR5443684,SRX2733019,SRS2120916,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 2,GSM2574372,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574372,GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq,GSM2574372,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M2_S4_L001_R1_001.fastq.gz,fastq,1110761224.0,14715439.0,GSM2574372 r1,0:75.48 1:0,A:275638341;C:274879264;G:260426963;T:299738013;N:78643,75,0,,,275638341,274879264,260426963,299738013,78643,SRX2733019,SRS2120916,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93377,,0.0583,,0.73697,,0.503,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42146,SRR5443685,SRX2733019,SRS2120916,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 2,GSM2574372,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574372,GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq,GSM2574372,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M2_S4_L002_R1_001.fastq.gz,fastq,1096460187.0,14525794.0,GSM2574372 r2,0:75.48 1:0,A:271912949;C:271463678;G:257186071;T:295823949;N:73540,75,0,,,271912949,271463678,257186071,295823949,73540,SRX2733019,SRS2120916,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.9322,,0.05825,,0.74054,,0.50344,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42147,SRR5443686,SRX2733019,SRS2120916,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 2,GSM2574372,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574372,GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq,GSM2574372,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M2_S4_L003_R1_001.fastq.gz,fastq,1091010366.0,14453885.0,GSM2574372 r3,0:75.48 1:0,A:272182496;C:270174883;G:255585422;T:293013773;N:53792,75,0,,,272182496,270174883,255585422,293013773,53792,SRX2733019,SRS2120916,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93152,,0.05837,,0.74168,,0.50083,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42148,SRR5443687,SRX2733019,SRS2120916,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 2,GSM2574372,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574372,GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq,GSM2574372,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M2_S4_L004_R1_001.fastq.gz,fastq,1094982987.0,14506489.0,GSM2574372 r4,0:75.48 1:0,A:272880331;C:271041484;G:256630523;T:294374054;N:56595,75,0,,,272880331,271041484,256630523,294374054,56595,SRX2733019,SRS2120916,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93087,,0.05679,,0.73791,,0.51669,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42149,SRR5443680,SRX2733018,SRS2120918,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 1,GSM2574371,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574371,GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq,GSM2574371,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M1_S2_L001_R1_001.fastq.gz,fastq,1191104867.0,15788220.0,GSM2574371 r1,0:75.44 1:0,A:291253611;C:297887900;G:280714676;T:321180057;N:68623,75,0,,,291253611,297887900,280714676,321180057,68623,SRX2733018,SRS2120918,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93937,,0.05486,,0.73841,,0.50505,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42150,SRR5443681,SRX2733018,SRS2120918,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 1,GSM2574371,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574371,GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq,GSM2574371,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M1_S2_L002_R1_001.fastq.gz,fastq,1175231750.0,15577911.0,GSM2574371 r2,0:75.44 1:0,A:287141469;C:293942288;G:277159611;T:316919071;N:69311,75,0,,,287141469,293942288,277159611,316919071,69311,SRX2733018,SRS2120918,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93883,,0.05461,,0.73841,,0.50615,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42151,SRR5443682,SRX2733018,SRS2120918,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 1,GSM2574371,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574371,GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq,GSM2574371,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M1_S2_L003_R1_001.fastq.gz,fastq,1170671016.0,15517791.0,GSM2574371 r3,0:75.44 1:0,A:287726896;C:292922993;G:275775803;T:314197498;N:47826,75,0,,,287726896,292922993,275775803,314197498,47826,SRX2733018,SRS2120918,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93571,,0.05459,,0.74168,,0.50894,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42152,SRR5443683,SRX2733018,SRS2120918,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell mutant 1,GSM2574371,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant,48hpf zebrafish FAC sorted endothelial cell mutant 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:mafba uq4bh mutant,GSM2574371,GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq,GSM2574371,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,M1_S2_L004_R1_001.fastq.gz,fastq,1174626578.0,15569716.0,GSM2574371 r4,0:75.44 1:0,A:288367287;C:293885435;G:276774483;T:315550752;N:48621,75,0,,,288367287,293885435,276774483,315550752,48621,SRX2733018,SRS2120918,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93712,,0.05466,,0.73969,,0.50987,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42153,SRR5443676,SRX2733017,SRS2120915,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 3,GSM2574370,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574370,GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq,GSM2574370,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S3_S5_L001_R1_001.fastq.gz,fastq,1200317760.0,15909907.0,GSM2574370 r1,0:75.44 1:0,A:296365402;C:297373974;G:283266985;T:323244649;N:66750,75,0,,,296365402,297373974,283266985,323244649,66750,SRX2733017,SRS2120915,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92986,,0.05547,,0.72805,,0.50801,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42154,SRR5443677,SRX2733017,SRS2120915,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 3,GSM2574370,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574370,GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq,GSM2574370,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S3_S5_L002_R1_001.fastq.gz,fastq,1186590046.0,15727830.0,GSM2574370 r2,0:75.45 1:0,A:292748835;C:294033369;G:280237781;T:319506249;N:63812,75,0,,,292748835,294033369,280237781,319506249,63812,SRX2733017,SRS2120915,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92874,,0.05356,,0.72839,,0.51335,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42155,SRR5443678,SRX2733017,SRS2120915,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 3,GSM2574370,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574370,GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq,GSM2574370,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S3_S5_L003_R1_001.fastq.gz,fastq,1179030774.0,15627890.0,GSM2574370 r3,0:75.44 1:0,A:292569213;C:292307681;G:278072717;T:316039886;N:41277,75,0,,,292569213,292307681,278072717,316039886,41277,SRX2733017,SRS2120915,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92502,,0.0542,,0.73129,,0.50553,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42156,SRR5443679,SRX2733017,SRS2120915,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 3,GSM2574370,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 3,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574370,GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq,GSM2574370,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S3_S5_L004_R1_001.fastq.gz,fastq,1186517148.0,15727062.0,GSM2574370 r4,0:75.44 1:0,A:294065343;C:294086528;G:279977232;T:318344594;N:43451,75,0,,,294065343,294086528,279977232,318344594,43451,SRX2733017,SRS2120915,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92801,,0.05486,,0.7263,,0.51617,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42157,SRR5443672,SRX2733016,SRS2120914,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 2,GSM2574369,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574369,GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq,GSM2574369,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S2_S3_L001_R1_001.fastq.gz,fastq,1118226721.0,14818796.0,GSM2574369 r1,0:75.46 1:0,A:277321886;C:276240373;G:264607012;T:299984813;N:72637,75,0,,,277321886,276240373,264607012,299984813,72637,SRX2733016,SRS2120914,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92813,,0.0608,,0.73511,,0.49445,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42158,SRR5443673,SRX2733016,SRS2120914,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 2,GSM2574369,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574369,GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq,GSM2574369,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S2_S3_L002_R1_001.fastq.gz,fastq,1097382503.0,14542648.0,GSM2574369 r2,0:75.46 1:0,A:271913618;C:271165534;G:259952446;T:294280610;N:70295,75,0,,,271913618,271165534,259952446,294280610,70295,SRX2733016,SRS2120914,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92628,,0.05901,,0.73434,,0.50436,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42159,SRR5443674,SRX2733016,SRS2120914,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 2,GSM2574369,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574369,GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq,GSM2574369,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S2_S3_L003_R1_001.fastq.gz,fastq,1100385244.0,14582533.0,GSM2574369 r3,0:75.46 1:0,A:274241238;C:272082346;G:260277831;T:293731839;N:51990,75,0,,,274241238,272082346,260277831,293731839,51990,SRX2733016,SRS2120914,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92524,,0.06015,,0.73805,,0.50957,,71,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42160,SRR5443675,SRX2733016,SRS2120914,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 2,GSM2574369,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 2,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574369,GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq,GSM2574369,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S2_S3_L004_R1_001.fastq.gz,fastq,1100058192.0,14577978.0,GSM2574369 r4,0:75.46 1:0,A:273957130;C:271919703;G:260365193;T:293764097;N:52069,75,0,,,273957130,271919703,260365193,293764097,52069,SRX2733016,SRS2120914,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.92546,,0.06173,,0.73985,,0.52271,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42161,SRR5443668,SRX2733015,SRS2120913,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 1,GSM2574368,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574368,GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq,GSM2574368,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S1_S1_L001_R1_001.fastq.gz,fastq,1086391308.0,14398072.0,GSM2574368 r1,0:75.45 1:0,A:265407098;C:273473167;G:256935933;T:290517430;N:57680,75,0,,,265407098,273473167,256935933,290517430,57680,SRX2733015,SRS2120913,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93916,,0.05822,,0.73785,,0.51199,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42162,SRR5443669,SRX2733015,SRS2120913,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 1,GSM2574368,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574368,GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq,GSM2574368,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S1_S1_L002_R1_001.fastq.gz,fastq,1073108602.0,14221959.0,GSM2574368 r2,0:75.45 1:0,A:261964537;C:270187564;G:253958473;T:286941827;N:56201,75,0,,,261964537,270187564,253958473,286941827,56201,SRX2733015,SRS2120913,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93746,,0.05835,,0.73734,,0.50609,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42163,SRR5443670,SRX2733015,SRS2120913,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 1,GSM2574368,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574368,GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq,GSM2574368,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S1_S1_L003_R1_001.fastq.gz,fastq,1064653834.0,14110138.0,GSM2574368 r3,0:75.45 1:0,A:261657368;C:268193214;G:251551872;T:283215565;N:35815,75,0,,,261657368,268193214,251551872,283215565,35815,SRX2733015,SRS2120913,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93651,,0.05738,,0.74042,,0.51489,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
42164,SRR5443671,SRX2733015,SRS2120913,SRP103805,PRJNA382558,mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.,GSE97649,Transcriptome Analysis,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate  with 6 brains used per samples. Overall design: wild type vs mutant,,pubmed:26253536,,48hpf zebrafish FAC sorted endothelial cell wt 1,GSM2574368,,tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype,48hpf zebrafish FAC sorted endothelial cell wt 1,adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample,purified endothelial cell,,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,,transgene:kdrl eGFP|genotype:wildtype,GSM2574368,GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq,GSM2574368,,1,48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2574368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP103805,,,S1_S1_L004_R1_001.fastq.gz,fastq,1072543375.0,14214599.0,GSM2574368 r4,0:75.45 1:0,A:263268340;C:270054371;G:253632532;T:285551360;N:36772,75,0,,,263268340,270054371,253632532,285551360,36772,SRX2733015,SRS2120913,SRA553927,GEO,Australian Institute for Bioengineering and Nanotechnology,1,0.93658,,0.05706,,0.73935,,0.5115,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2017-04-11,Hatching,Embryo,Endothelium,Cardiovascular System
47740,SRR6848349,SRX3803619,SRS3055252,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,hhex overexpression rep2,GSM3045716,,tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells,hhex overexpression rep2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045716,GSM3045716: hhex overexpression rep2; Danio rerio; RNA Seq,GSM3045716,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045716,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_OE_2_R1.fastq.gz,fastq,2514724985.0,34768823.0,GSM3045716 r1,0:72.33 1:0,A:565805246;C:704077993;G:741187599;T:503446013;N:208134,72,0,,,565805246,704077993,741187599,503446013,208134,SRX3803619,SRS3055252,SRA667127,GEO,MPI for heart and lung research,1,0.94763,,0.26354,,0.80702,,0.62768,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
47741,SRR6848348,SRX3803618,SRS3055251,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,hhex overexpression rep1,GSM3045715,,tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells,hhex overexpression rep1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045715,GSM3045715: hhex overexpression rep1; Danio rerio; RNA Seq,GSM3045715,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045715,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_OE_1_R1.fastq.gz,fastq,2201523348.0,30479961.0,GSM3045715 r1,0:72.23 1:0,A:510844407;C:602803512;G:634953285;T:452682176;N:239968,72,0,,,510844407,602803512,634953285,452682176,239968,SRX3803618,SRS3055251,SRA667127,GEO,MPI for heart and lung research,1,0.94219,,0.27653,,0.80466,,0.66516,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
47742,SRR6848347,SRX3803617,SRS3055250,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,hhex mutant rep2,GSM3045714,,tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells,hhex mutant rep2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045714,GSM3045714: hhex mutant rep2; Danio rerio; RNA Seq,GSM3045714,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045714,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_Mut_2_R1.fastq.gz,fastq,2377033794.0,32865413.0,GSM3045714 r1,0:72.33 1:0,A:531221225;C:668093793;G:704926379;T:472544720;N:247677,72,0,,,531221225,668093793,704926379,472544720,247677,SRX3803617,SRS3055250,SRA667127,GEO,MPI for heart and lung research,1,0.93202,,0.25789,,0.81617,,0.66408,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
47743,SRR6848346,SRX3803616,SRS3055249,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,hhex mutant rep1,GSM3045713,,tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells,hhex mutant rep1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045713,GSM3045713: hhex mutant rep1; Danio rerio; RNA Seq,GSM3045713,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045713,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_Mut_1_R1.fastq.gz,fastq,2492708175.0,34527636.0,GSM3045713 r1,0:72.19 1:0,A:555859455;C:702003394;G:740775583;T:493818885;N:250858,72,0,,,555859455,702003394,740775583,493818885,250858,SRX3803616,SRS3055249,SRA667127,GEO,MPI for heart and lung research,1,0.93924,,0.25343,,0.81889,,0.6311,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
47744,SRR6848345,SRX3803615,SRS3055248,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,Sibling rep2,GSM3045712,,tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells,Sibling rep2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045712,GSM3045712: Sibling rep2; Danio rerio; RNA Seq,GSM3045712,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045712,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_WT_2_R1.fastq.gz,fastq,2451974351.0,33830383.0,GSM3045712 r1,0:72.48 1:0,A:557370317;C:679644672;G:720300776;T:494468929;N:189657,72,0,,,557370317,679644672,720300776,494468929,189657,SRX3803615,SRS3055248,SRA667127,GEO,MPI for heart and lung research,1,0.91674,,0.25327,,0.80868,,0.70337,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
47745,SRR6848344,SRX3803614,SRS3055247,SRP135898,PRJNA438687,Transcriptome profiling of endothelial cells from wild type  hhex mutants and hhex overexpression zebrafish embryos,GSE111963,Transcriptome Analysis,We used high throughput sequencing to identify differential expression in siblings  hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings  hhex mutants and hhex overexpression at 48 hpf,,pubmed:30006544,,Sibling rep1,GSM3045711,,tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells,Sibling rep1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of +  1.5 log2 + 0.59  a maximum Benjamini Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak,FACS sorted endothelial cells,,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,,genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells,GSM3045711,GSM3045711: Sibling rep1; Danio rerio; RNA Seq,GSM3045711,,1,For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf  embryos were divided based on the absence of PLs.  Then  embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in minimum of 30M reads per library with 1x75bp single end setup.,GEO Accession:GSM3045711,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP135898,,,Sebastien_WT_1_R1.fastq.gz,fastq,2685019288.0,37185023.0,GSM3045711 r1,0:72.21 1:0,A:629322492;C:731250924;G:769793846;T:554311522;N:340504,72,0,,,629322492,731250924,769793846,554311522,340504,SRX3803614,SRS3055247,SRA667127,GEO,MPI for heart and lung research,1,0.90551,,0.24697,,0.80695,,0.65765,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Germany,2018-03-16,Hatching,Embryo,Endothelium,Cardiovascular System
66760,SRR16573983,SRX12775941,SRS10721245,SRP343153,PRJNA774550,Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells,GSE186565,Transcriptome Analysis,Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs  mCherry+ ECs and double positive cells undergoing EHT. Following the sort  cells underwent standard 10x encapsulation.,,pubmed:34919128,,Vegfc MO,GSM5655701,,tissue:Endothelial Cells  HSPCs|treatment:Vegfc MO|strain:flk:mCherry; cd41:gfp|age:52 hpf,Vegfc MO,Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment  filtering  barcode counting  and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix,Endothelial Cells  HSPCs,Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq,Embryos were maintained in E3 embryo medium until 52 hpf,treatment:Vegfc MO|strain:flk:mCherry;cd41:gfp|age:52 hpf,GSM5655701,GSM5655701: Vegfc MO; Danio rerio; RNA Seq,GSM5655701 r1,GSM5655701,1,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343153,,,VegfcMo_S3_L001_R1_001.fastq.gz VegfcMo_S3_L001_R2_001.fastq.gz,fastq fastq,13667302233.0,116814549.0,GSM5655701 r1,0:28 1:89,A:3845447410;C:3000770206;G:3051184574;T:3769610622;N:289421,28,89,,,3845447410,3000770206,3051184574,3769610622,289421,SRX12775941,SRS10721245,SRA1317383,"Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison","Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.00828,0.92236,0.00351,0.1852,0.99036,0.75982,0.37956,0.50465,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2021-10-26,Hatching,Embryo,Endothelium,Cardiovascular System
66761,SRR16573984,SRX12775941,SRS10721245,SRP343153,PRJNA774550,Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells,GSE186565,Transcriptome Analysis,Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs  mCherry+ ECs and double positive cells undergoing EHT. Following the sort  cells underwent standard 10x encapsulation.,,pubmed:34919128,,Vegfc MO,GSM5655701,,tissue:Endothelial Cells  HSPCs|treatment:Vegfc MO|strain:flk:mCherry; cd41:gfp|age:52 hpf,Vegfc MO,Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment  filtering  barcode counting  and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix,Endothelial Cells  HSPCs,Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq,Embryos were maintained in E3 embryo medium until 52 hpf,treatment:Vegfc MO|strain:flk:mCherry;cd41:gfp|age:52 hpf,GSM5655701,GSM5655701: Vegfc MO; Danio rerio; RNA Seq,GSM5655701 r1,GSM5655701,1,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343153,,,VegfcMo_S3_L002_R1_001.fastq.gz VegfcMo_S3_L002_R2_001.fastq.gz,fastq fastq,13683498777.0,116952981.0,GSM5655701 r2,0:28 1:89,A:3849019312;C:3005132517;G:3056752429;T:3772346961;N:247558,28,89,,,3849019312,3005132517,3056752429,3772346961,247558,SRX12775941,SRS10721245,SRA1317383,"Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison","Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.00801,0.92192,0.00324,0.18499,0.99099,0.75877,0.37068,0.50141,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2021-10-26,Hatching,Embryo,Endothelium,Cardiovascular System
66762,SRR16573985,SRX12775940,SRS10721244,SRP343153,PRJNA774550,Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells,GSE186565,Transcriptome Analysis,Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs  mCherry+ ECs and double positive cells undergoing EHT. Following the sort  cells underwent standard 10x encapsulation.,,pubmed:34919128,,Uninjected,GSM5655700,,tissue:Endothelial Cells  HSPCs|treatment:Uninjected|strain:flk:mCherry; cd41:gfp|age:52 hpf,Uninjected,Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment  filtering  barcode counting  and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix,Endothelial Cells  HSPCs,Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq,Embryos were maintained in E3 embryo medium until 52 hpf,treatment:Uninjected|strain:flk:mCherry;cd41:gfp|age:52 hpf,GSM5655700,GSM5655700: Uninjected; Danio rerio; RNA Seq,GSM5655700 r1,GSM5655700,1,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343153,,,UnInj2_S2_L001_R1_001.fastq.gz UnInj2_S2_L001_R2_001.fastq.gz,fastq fastq,23657101884.0,202197452.0,GSM5655700 r1,0:28 1:89,A:6762677862;C:5216362851;G:5376327033;T:6301229587;N:504551,28,89,,,6762677862,5216362851,5376327033,6301229587,504551,SRX12775940,SRS10721244,SRA1317383,"Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison","Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.00742,0.92485,0.00268,0.17441,0.99196,0.76497,0.33369,0.53366,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2021-10-26,Hatching,Embryo,Endothelium,Cardiovascular System
66763,SRR16573986,SRX12775940,SRS10721244,SRP343153,PRJNA774550,Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells,GSE186565,Transcriptome Analysis,Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs  mCherry+ ECs and double positive cells undergoing EHT. Following the sort  cells underwent standard 10x encapsulation.,,pubmed:34919128,,Uninjected,GSM5655700,,tissue:Endothelial Cells  HSPCs|treatment:Uninjected|strain:flk:mCherry; cd41:gfp|age:52 hpf,Uninjected,Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment  filtering  barcode counting  and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix,Endothelial Cells  HSPCs,Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq,Embryos were maintained in E3 embryo medium until 52 hpf,treatment:Uninjected|strain:flk:mCherry;cd41:gfp|age:52 hpf,GSM5655700,GSM5655700: Uninjected; Danio rerio; RNA Seq,GSM5655700 r1,GSM5655700,1,Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized  dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343153,,,UnInj2_S2_L002_R1_001.fastq.gz UnInj2_S2_L002_R2_001.fastq.gz,fastq fastq,23583414231.0,201567643.0,GSM5655700 r2,0:28 1:89,A:6738316424;C:5202021444;G:5363779316;T:6278870685;N:426362,28,89,,,6738316424,5202021444,5363779316,6278870685,426362,SRX12775940,SRS10721244,SRA1317383,"Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison","Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.00772,0.92365,0.0027,0.17244,0.99091,0.76481,0.30847,0.53164,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2021-10-26,Hatching,Embryo,Endothelium,Cardiovascular System
69000,SRR18290758,SRX14428461,SRS12237031,SRP363388,PRJNA814612,Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites,GSE198221,Other,The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells HUVEC exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown Overall design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA Seq  ATAC Seq and H3K27ac ChIP Seq. Blood flow was stopped in zebrafish embryos 48 hpf for 4 h and endothelial cells were used for RNA Seq,,pubmed:35314737,,Zebrafish Flow Block RNA Seq Rep2,GSM5941049,,tissue:Endothelial cells|treatment:Flow Block for 4 h|transgene:Tgkdrl:H2B EGFPmu125,Zebrafish Flow Block RNA Seq Rep2,Sequencing reads were aligned to hg19 human or danRer10 zebrafish genomes RNA Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq ChIP Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich https://github.com/jsh58/Genrich applying the following parameters: genrich  v  e Y MT  E blacklist.bed  t Sample1ChIP.bam  Sample2ChIP.bam  c Sample1Input.bam  Sample2Input.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis. ATAC Seq. Sequencing reads were mapped with Bowtie2  downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC Seq mode using the following parameters: genrich  j  v  y  r  e Y MT  E blacklist.bed  t Sample1.bam  Sample2.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis. ChIP Seq and ATAC Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth Assembly: hg19 Assembly: danRer10,Endothelial cells,The maximum flow of 18 dyn/cm2 was achieved by computer controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone PVP within ten minutes ramp function and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system BTF system; MOS Technologies at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator. 48 hpf Tgkdrl:H2B EGFPmu122 zebrafish embryos were dechorionated at 48 hpf using pronase and treated for 4 h with nifedipine 12.5 nM  Biomol  # Cay11106 and tricaine 1.3 mM  Sigma Aldrich  # A5040 to stop the heart beat or with a corresponding amount of DMSO as a control.,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks’Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer’s solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,HUVEC were seeded on 6 cm BTF glass plates coated with cross linked gelatin and cultured to confluence approximately 105 cells/cm2 in EC growth medium. Zebrafish were grown and crossed under standard conditions,treatment:Flow Block for 4 h|transgene:Tgkdrl:H2B EGFPmu125,GSM5941049,GSM5941049: Zebrafish Flow Block RNA Seq Rep2; Danio rerio; RNA Seq,GSM5941049 r1,GSM5941049,1,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks'Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer's solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,SRP363388,,loader:fastq load.py,FLOWBLOCK2_S4_L001_R1_001.fastq FLOWBLOCK2_S4_L001_R2_001.fastq,fastq fastq,805667987.0,5200034.0,GSM5941049 r1,0:77.50 1:77.43,A:210091360;C:190624392;G:188960497;T:215980412;N:11326,77,77,,,210091360,190624392,188960497,215980412,11326,SRX14428461,SRS12237031,SRA1385237,"Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA","Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA",2,0.93751,0.9424,0.28298,0.28145,0.74103,0.74119,0.63737,0.6474,78,78,B,B,biological fallback assumption,illumina,miseq,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2022-03-09,Hatching,Embryo,Endothelium,Cardiovascular System
69001,SRR18290759,SRX14428460,SRS12237030,SRP363388,PRJNA814612,Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites,GSE198221,Other,The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells HUVEC exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown Overall design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA Seq  ATAC Seq and H3K27ac ChIP Seq. Blood flow was stopped in zebrafish embryos 48 hpf for 4 h and endothelial cells were used for RNA Seq,,pubmed:35314737,,Zebrafish Flow Block RNA Seq Rep1,GSM5941048,,tissue:Endothelial cells|treatment:Flow Block for 4 h|transgene:Tgkdrl:H2B EGFPmu124,Zebrafish Flow Block RNA Seq Rep1,Sequencing reads were aligned to hg19 human or danRer10 zebrafish genomes RNA Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq ChIP Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich https://github.com/jsh58/Genrich applying the following parameters: genrich  v  e Y MT  E blacklist.bed  t Sample1ChIP.bam  Sample2ChIP.bam  c Sample1Input.bam  Sample2Input.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis. ATAC Seq. Sequencing reads were mapped with Bowtie2  downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC Seq mode using the following parameters: genrich  j  v  y  r  e Y MT  E blacklist.bed  t Sample1.bam  Sample2.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis. ChIP Seq and ATAC Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth Assembly: hg19 Assembly: danRer10,Endothelial cells,The maximum flow of 18 dyn/cm2 was achieved by computer controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone PVP within ten minutes ramp function and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system BTF system; MOS Technologies at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator. 48 hpf Tgkdrl:H2B EGFPmu122 zebrafish embryos were dechorionated at 48 hpf using pronase and treated for 4 h with nifedipine 12.5 nM  Biomol  # Cay11106 and tricaine 1.3 mM  Sigma Aldrich  # A5040 to stop the heart beat or with a corresponding amount of DMSO as a control.,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks’Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer’s solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,HUVEC were seeded on 6 cm BTF glass plates coated with cross linked gelatin and cultured to confluence approximately 105 cells/cm2 in EC growth medium. Zebrafish were grown and crossed under standard conditions,treatment:Flow Block for 4 h|transgene:Tgkdrl:H2B EGFPmu124,GSM5941048,GSM5941048: Zebrafish Flow Block RNA Seq Rep1; Danio rerio; RNA Seq,GSM5941048 r1,GSM5941048,1,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks'Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer's solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,SRP363388,,loader:fastq load.py,FLOWBLOCK1_S2_L001_R1_001.fastq FLOWBLOCK1_S2_L001_R2_001.fastq,fastq fastq,990262487.0,6392689.0,GSM5941048 r1,0:77.50 1:77.41,A:260942015;C:231680705;G:228939024;T:268680312;N:20431,77,77,,,260942015,231680705,228939024,268680312,20431,SRX14428460,SRS12237030,SRA1385237,"Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA","Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA",2,0.92713,0.93004,0.24287,0.24411,0.72216,0.72374,0.63185,0.62673,78,78,B,B,biological fallback assumption,illumina,miseq,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2022-03-09,Hatching,Embryo,Endothelium,Cardiovascular System
69002,SRR18290760,SRX14428459,SRS12237029,SRP363388,PRJNA814612,Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites,GSE198221,Other,The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells HUVEC exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown Overall design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA Seq  ATAC Seq and H3K27ac ChIP Seq. Blood flow was stopped in zebrafish embryos 48 hpf for 4 h and endothelial cells were used for RNA Seq,,pubmed:35314737,,Zebrafish Control RNA Seq Rep2,GSM5941047,,tissue:Endothelial cells|treatment:DMSO|transgene:Tgkdrl:H2B EGFPmu123,Zebrafish Control RNA Seq Rep2,Sequencing reads were aligned to hg19 human or danRer10 zebrafish genomes RNA Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq ChIP Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich https://github.com/jsh58/Genrich applying the following parameters: genrich  v  e Y MT  E blacklist.bed  t Sample1ChIP.bam  Sample2ChIP.bam  c Sample1Input.bam  Sample2Input.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis. ATAC Seq. Sequencing reads were mapped with Bowtie2  downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC Seq mode using the following parameters: genrich  j  v  y  r  e Y MT  E blacklist.bed  t Sample1.bam  Sample2.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis. ChIP Seq and ATAC Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth Assembly: hg19 Assembly: danRer10,Endothelial cells,The maximum flow of 18 dyn/cm2 was achieved by computer controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone PVP within ten minutes ramp function and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system BTF system; MOS Technologies at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator. 48 hpf Tgkdrl:H2B EGFPmu122 zebrafish embryos were dechorionated at 48 hpf using pronase and treated for 4 h with nifedipine 12.5 nM  Biomol  # Cay11106 and tricaine 1.3 mM  Sigma Aldrich  # A5040 to stop the heart beat or with a corresponding amount of DMSO as a control.,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks’Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer’s solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,HUVEC were seeded on 6 cm BTF glass plates coated with cross linked gelatin and cultured to confluence approximately 105 cells/cm2 in EC growth medium. Zebrafish were grown and crossed under standard conditions,treatment:DMSO|transgene:Tgkdrl:H2B EGFPmu123,GSM5941047,GSM5941047: Zebrafish Control RNA Seq Rep2; Danio rerio; RNA Seq,GSM5941047 r1,GSM5941047,1,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks'Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer's solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,SRP363388,,loader:fastq load.py,DMSO2_S3_L001_R1_001.fastq DMSO2_S3_L001_R2_001.fastq,fastq fastq,971498292.0,6271128.0,GSM5941047 r1,0:77.50 1:77.41,A:260144407;C:222584067;G:221327331;T:267428497;N:13990,77,77,,,260144407,222584067,221327331,267428497,13990,SRX14428459,SRS12237029,SRA1385237,"Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA","Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA",2,0.93591,0.9398,0.22625,0.22749,0.7163,0.71685,0.59773,0.59563,78,78,B,B,biological fallback assumption,illumina,miseq,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2022-03-09,Hatching,Embryo,Endothelium,Cardiovascular System
69003,SRR18290761,SRX14428458,SRS12237028,SRP363388,PRJNA814612,Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites,GSE198221,Other,The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells HUVEC exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown Overall design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA Seq  ATAC Seq and H3K27ac ChIP Seq. Blood flow was stopped in zebrafish embryos 48 hpf for 4 h and endothelial cells were used for RNA Seq,,pubmed:35314737,,Zebrafish Control RNA Seq Rep1,GSM5941046,,tissue:Endothelial cells|treatment:DMSO|transgene:Tgkdrl:H2B EGFPmu122,Zebrafish Control RNA Seq Rep1,Sequencing reads were aligned to hg19 human or danRer10 zebrafish genomes RNA Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq ChIP Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich https://github.com/jsh58/Genrich applying the following parameters: genrich  v  e Y MT  E blacklist.bed  t Sample1ChIP.bam  Sample2ChIP.bam  c Sample1Input.bam  Sample2Input.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis. ATAC Seq. Sequencing reads were mapped with Bowtie2  downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC Seq mode using the following parameters: genrich  j  v  y  r  e Y MT  E blacklist.bed  t Sample1.bam  Sample2.bam  o Sample.narrowPeak  k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis. ChIP Seq and ATAC Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth Assembly: hg19 Assembly: danRer10,Endothelial cells,The maximum flow of 18 dyn/cm2 was achieved by computer controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone PVP within ten minutes ramp function and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system BTF system; MOS Technologies at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator. 48 hpf Tgkdrl:H2B EGFPmu122 zebrafish embryos were dechorionated at 48 hpf using pronase and treated for 4 h with nifedipine 12.5 nM  Biomol  # Cay11106 and tricaine 1.3 mM  Sigma Aldrich  # A5040 to stop the heart beat or with a corresponding amount of DMSO as a control.,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks’Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer’s solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,HUVEC were seeded on 6 cm BTF glass plates coated with cross linked gelatin and cultured to confluence approximately 105 cells/cm2 in EC growth medium. Zebrafish were grown and crossed under standard conditions,treatment:DMSO|transgene:Tgkdrl:H2B EGFPmu122,GSM5941046,GSM5941046: Zebrafish Control RNA Seq Rep1; Danio rerio; RNA Seq,GSM5941046 r1,GSM5941046,1,RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min  sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at  80°C for 2 min. postwards  embryos were washed twice with 1x Hanks'Balanced Salt Solution HBSS  Gibco  # 14185 052and deyolked with calcium free Ringer's solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash  cells were resuspended in 1x HBSS  passed through a 40 m nylon filter to obtain a single cell suspension  which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit  Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto  Nat Met  2013,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,SRP363388,,loader:fastq load.py,DMSO1_S1_L001_R1_001.fastq DMSO1_S1_L001_R2_001.fastq,fastq fastq,1241823302.0,8016001.0,GSM5941046 r1,0:77.51 1:77.41,A:328337938;C:289285295;G:287437001;T:336735414;N:27654,77,77,,,328337938,289285295,287437001,336735414,27654,SRX14428458,SRS12237028,SRA1385237,"Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA","Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA",2,0.93546,0.93858,0.24555,0.24639,0.71494,0.71508,0.60726,0.60144,78,78,B,B,biological fallback assumption,illumina,miseq,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2022-03-09,Hatching,Embryo,Endothelium,Cardiovascular System