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
33669,SRR30530658,SRX25954305,SRS22536191,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，high glucose,GSM8494124,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，high glucose,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494124,GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq,GSM8494124 r1,GSM8494124,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz,fastq fastq,196891371600.0,656304572.0,GSM8494124 r1,0:150 1:150,A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323,150,150,,,46034913013,37262343828,60636104680,52955473756,2536323,SRX25954305,SRS22536191,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33670,SRR30530659,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz,fastq fastq,18351420300.0,61171401.0,GSM8494123 r1,0:150 1:150,A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607,150,150,,,3872504772,3434009784,6583451920,4461384217,69607,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33671,SRR30530660,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz,fastq fastq,36386960400.0,121289868.0,GSM8494123 r2,0:150 1:150,A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278,150,150,,,8890006445,6974694151,10814990376,9707137150,132278,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33672,SRR30530661,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz,fastq fastq,44811813000.0,149372710.0,GSM8494123 r3,0:150 1:150,A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370,150,150,,,10939691275,8613307673,13332283843,11926366839,163370,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33673,SRR30530662,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz,fastq fastq,22587582300.0,75291941.0,GSM8494123 r4,0:150 1:150,A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737,150,150,,,4762937825,4235264474,8108549401,5480746863,83737,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33674,SRR30530663,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz,fastq fastq,31458502200.0,104861674.0,GSM8494123 r5,0:150 1:150,A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751,150,150,,,7597642424,6175910515,9377029875,8307805635,113751,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33675,SRR30530664,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz,fastq fastq,15812987400.0,52709958.0,GSM8494123 r6,0:150 1:150,A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817,150,150,,,3317721700,3009997461,5662825685,3822382737,59817,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33676,SRR30530665,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz,fastq fastq,19472976900.0,64909923.0,GSM8494123 r7,0:150 1:150,A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183,150,150,,,4109297307,3636046624,6996008921,4731548865,75183,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33677,SRR30530666,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz,fastq fastq,39005746200.0,130019154.0,GSM8494123 r8,0:150 1:150,A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785,150,150,,,9542890616,7456459618,11598648802,10407604379,142785,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
41681,SRR5119926,SRX2435201,SRS1870197,SRP095331,PRJNA358009,CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1],GSE92542,Transcriptome Analysis,The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.,parent bioproject:PRJNA358001,pubmed:28351983,,wt clutch2,GSM2432105,,tissue:endothelial cells|cell type:endothelial cells,wt clutch2,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample,endothelial cells,,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,Zebrafish embryos were grown under standard conditions in a 28 degree incubator.,cell type:endothelial cells,GSM2432105,GSM2432105: wt clutch2; Danio rerio; RNA Seq,GSM2432105,,1,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,GEO Accession:GSM2432105,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP095331,,,BB-IL8-7_GATCAG_R2.fastq.gz BB-IL8-7_GATCAG_R1.fastq.gz,fastq fastq,6054362200.0,30271811.0,GSM2432105 r1,0:100 1:100,A:1586036726;C:1442511502;G:1449390272;T:1575855416;N:568284,100,100,,,1586036726,1442511502,1449390272,1575855416,568284,SRX2435201,SRS1870197,SRA505250,GEO,"Oncology/Hematology, Boston Children's Hospital",2,0.68659,0.68507,0.22283,0.22137,0.76067,0.76343,0.57225,0.58743,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,unknown,unknown,,United States,2016-12-19,Undetermined,Embryo,Endothelium,Cardiovascular System
41682,SRR5119925,SRX2435200,SRS1870195,SRP095331,PRJNA358009,CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1],GSE92542,Transcriptome Analysis,The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.,parent bioproject:PRJNA358001,pubmed:28351983,,wt clutch1,GSM2432104,,tissue:endothelial cells|cell type:endothelial cells,wt clutch1,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample,endothelial cells,,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,Zebrafish embryos were grown under standard conditions in a 28 degree incubator.,cell type:endothelial cells,GSM2432104,GSM2432104: wt clutch1; Danio rerio; RNA Seq,GSM2432104,,1,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,GEO Accession:GSM2432104,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP095331,,,BB-IL8-3_TGACCA_R1.fastq.gz BB-IL8-3_TGACCA_R2.fastq.gz,fastq fastq,4718160000.0,23590800.0,GSM2432104 r1,0:100 1:100,A:1285175152;C:1075055485;G:1078285328;T:1279202852;N:441183,100,100,,,1285175152,1075055485,1078285328,1279202852,441183,SRX2435200,SRS1870195,SRA505250,GEO,"Oncology/Hematology, Boston Children's Hospital",2,0.79676,0.7947,0.26445,0.26272,0.71652,0.71924,0.55157,0.55957,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,unknown,unknown,,United States,2016-12-19,Undetermined,Embryo,Endothelium,Cardiovascular System
41683,SRR5119924,SRX2435199,SRS1870196,SRP095331,PRJNA358009,CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1],GSE92542,Transcriptome Analysis,The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.,parent bioproject:PRJNA358001,pubmed:28351983,,kdrl:cxcr1 clutch2,GSM2432103,,tissue:endothelial cells|cell type:endothelial cells,kdrl:cxcr1 clutch2,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample,endothelial cells,,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,Zebrafish embryos were grown under standard conditions in a 28 degree incubator.,cell type:endothelial cells,GSM2432103,GSM2432103: kdrl:cxcr1 clutch2; Danio rerio; RNA Seq,GSM2432103,,1,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,GEO Accession:GSM2432103,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP095331,,,BB-IL8-5_GCCAAT_R1.fastq.gz BB-IL8-5_GCCAAT_R2.fastq.gz,fastq fastq,4575871400.0,22879357.0,GSM2432103 r1,0:100 1:100,A:1212272291;C:1077863805;G:1079802103;T:1205507838;N:425363,100,100,,,1212272291,1077863805,1079802103,1205507838,425363,SRX2435199,SRS1870196,SRA505250,GEO,"Oncology/Hematology, Boston Children's Hospital",2,0.79788,0.79581,0.25639,0.25339,0.74888,0.75195,0.55512,0.56401,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,unknown,unknown,,United States,2016-12-19,Undetermined,Embryo,Endothelium,Cardiovascular System
41684,SRR5119923,SRX2435198,SRS1870193,SRP095331,PRJNA358009,CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1],GSE92542,Transcriptome Analysis,The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.,parent bioproject:PRJNA358001,pubmed:28351983,,kdrl:cxcr1 clutch1,GSM2432102,,tissue:endothelial cells|cell type:endothelial cells,kdrl:cxcr1 clutch1,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample,endothelial cells,,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,Zebrafish embryos were grown under standard conditions in a 28 degree incubator.,cell type:endothelial cells,GSM2432102,GSM2432102: kdrl:cxcr1 clutch1; Danio rerio; RNA Seq,GSM2432102,,1,Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.,GEO Accession:GSM2432102,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP095331,,,BB-IL8-1_ATCACG_R1.fastq.gz BB-IL8-1_ATCACG_R2.fastq.gz,fastq fastq,5384509000.0,26922545.0,GSM2432102 r1,0:100 1:100,A:1457197772;C:1237507818;G:1239484699;T:1449819489;N:499222,100,100,,,1457197772,1237507818,1239484699,1449819489,499222,SRX2435198,SRS1870193,SRA505250,GEO,"Oncology/Hematology, Boston Children's Hospital",2,0.80446,0.79238,0.24797,0.24691,0.72423,0.72681,0.57301,0.46021,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,unknown,unknown,,United States,2016-12-19,Undetermined,Embryo,Endothelium,Cardiovascular System
52764,SRR9207199,SRX5978265,SRS4884520,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep3,GSM3855057,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855057,GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq,GSM3855057,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855057,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_268_1_pair.fq.gz WTCHG_236896_268_2_pair.fq.gz,fastq fastq,1927186907.0,13135764.0,GSM3855057 r1,0:74.85 1:71.86,A:495349382;C:442938837;G:459765161;T:529104158;N:29369,74,71,,,495349382,442938837,459765161,529104158,29369,SRX5978265,SRS4884520,SRA894667,GEO,Oxford University,2,0.9511,0.71957,0.05876,0.04975,0.80322,0.83463,0.41847,0.47909,75,64,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52765,SRR9207200,SRX5978265,SRS4884520,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep3,GSM3855057,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855057,GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq,GSM3855057,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855057,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_268_1_pair.fq.gz WTCHG_236897_268_2_pair.fq.gz,fastq fastq,1909528693.0,13017658.0,GSM3855057 r2,0:74.82 1:71.87,A:490710971;C:436487071;G:453444216;T:528853285;N:33150,74,71,,,490710971,436487071,453444216,528853285,33150,SRX5978265,SRS4884520,SRA894667,GEO,Oxford University,2,0.94988,0.70903,0.05941,0.04918,0.80346,0.83597,0.42243,0.48127,74,69,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52766,SRR9207197,SRX5978264,SRS4884519,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep2,GSM3855056,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855056,GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq,GSM3855056,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_253_2_pair.fq.gz WTCHG_236896_253_1_pair.fq.gz,fastq fastq,2328318316.0,15846855.0,GSM3855056 r1,0:74.86 1:72.07,A:595900608;C:546479100;G:562297908;T:623605072;N:35628,74,72,,,595900608,546479100,562297908,623605072,35628,SRX5978264,SRS4884519,SRA894667,GEO,Oxford University,2,0.95426,0.78099,0.04531,0.04107,0.79285,0.81738,0.47636,0.47393,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52767,SRR9207198,SRX5978264,SRS4884519,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep2,GSM3855056,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855056,GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq,GSM3855056,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_253_1_pair.fq.gz WTCHG_236897_253_2_pair.fq.gz,fastq fastq,2302889916.0,15678935.0,GSM3855056 r2,0:74.83 1:72.05,A:589414837;C:537423117;G:553631542;T:622379721;N:40699,74,72,,,589414837,537423117,553631542,622379721,40699,SRX5978264,SRS4884519,SRA894667,GEO,Oxford University,2,0.95316,0.76729,0.04543,0.04,0.79368,0.81994,0.4793,0.45619,74,73,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52768,SRR9207195,SRX5978263,SRS4884518,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep1,GSM3855055,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855055,GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq,GSM3855055,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855055,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_246_1_pair.fq.gz WTCHG_236896_246_2_pair.fq.gz,fastq fastq,2117580563.0,14386411.0,GSM3855055 r1,0:74.87 1:72.33,A:541407670;C:500318189;G:514959635;T:560861522;N:33547,74,72,,,541407670,500318189,514959635,560861522,33547,SRX5978263,SRS4884518,SRA894667,GEO,Oxford University,2,0.95698,0.79806,0.0412,0.03838,0.79683,0.82073,0.4361,0.47246,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52769,SRR9207196,SRX5978263,SRS4884518,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DP R1hi rep1,GSM3855055,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,RNA seq MO DP R1hi rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected,GSM3855055,GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq,GSM3855055,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855055,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_246_1_pair.fq.gz WTCHG_236897_246_2_pair.fq.gz,fastq fastq,2093566860.0,14226227.0,GSM3855055 r2,0:74.83 1:72.33,A:535219614;C:492666345;G:507484718;T:558158640;N:37543,74,72,,,535219614,492666345,507484718,558158640,37543,SRX5978263,SRS4884518,SRA894667,GEO,Oxford University,2,0.95586,0.7889,0.04114,0.03868,0.79689,0.82104,0.43998,0.46953,74,47,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52770,SRR9207193,SRX5978262,SRS4884517,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep3,GSM3855054,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855054,GSM3855054: MO DN rep3; Danio rerio; RNA Seq,GSM3855054,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855054,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_269_1_pair.fq.gz WTCHG_236896_269_2_pair.fq.gz,fastq fastq,2046617161.0,13945847.0,GSM3855054 r1,0:74.83 1:71.93,A:534129043;C:466415284;G:478200001;T:567840465;N:32368,74,71,,,534129043,466415284,478200001,567840465,32368,SRX5978262,SRS4884517,SRA894667,GEO,Oxford University,2,0.94896,0.77373,0.08658,0.07153,0.73519,0.76715,0.49305,0.48341,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52771,SRR9207194,SRX5978262,SRS4884517,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep3,GSM3855054,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855054,GSM3855054: MO DN rep3; Danio rerio; RNA Seq,GSM3855054,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855054,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_269_1_pair.fq.gz WTCHG_236897_269_2_pair.fq.gz,fastq fastq,2013937570.0,13725739.0,GSM3855054 r2,0:74.79 1:71.93,A:525460437;C:456678849;G:468917277;T:562845673;N:35334,74,71,,,525460437,456678849,468917277,562845673,35334,SRX5978262,SRS4884517,SRA894667,GEO,Oxford University,2,0.94917,0.76456,0.08857,0.07125,0.73541,0.76777,0.49906,0.49093,74,44,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52772,SRR9207191,SRX5978261,SRS4884516,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep2,GSM3855053,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855053,GSM3855053: MO DN rep2; Danio rerio; RNA Seq,GSM3855053,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855053,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_254_1_pair.fq.gz WTCHG_236896_254_2_pair.fq.gz,fastq fastq,2491569443.0,17007413.0,GSM3855053 r1,0:74.84 1:71.66,A:650887336;C:562551977;G:579971830;T:698120812;N:37488,74,71,,,650887336,562551977,579971830,698120812,37488,SRX5978261,SRS4884516,SRA894667,GEO,Oxford University,2,0.95058,0.74758,0.08565,0.06922,0.74817,0.78344,0.49706,0.48533,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52773,SRR9207192,SRX5978261,SRS4884516,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep2,GSM3855053,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855053,GSM3855053: MO DN rep2; Danio rerio; RNA Seq,GSM3855053,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855053,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_254_1_pair.fq.gz WTCHG_236897_254_2_pair.fq.gz,fastq fastq,2467826388.0,16847563.0,GSM3855053 r2,0:74.80 1:71.67,A:644767348;C:554488060;G:572473532;T:696053759;N:43689,74,71,,,644767348,554488060,572473532,696053759,43689,SRX5978261,SRS4884516,SRA894667,GEO,Oxford University,2,0.95097,0.73759,0.0857,0.0679,0.74805,0.78307,0.50597,0.48761,74,59,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52774,SRR9207189,SRX5978260,SRS4884515,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep1,GSM3855052,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855052,GSM3855052: MO DN rep1; Danio rerio; RNA Seq,GSM3855052,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855052,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_247_1_pair.fq.gz WTCHG_236896_247_2_pair.fq.gz,fastq fastq,1764365530.0,12029530.0,GSM3855052 r1,0:74.84 1:71.83,A:466613214;C:395400217;G:407881798;T:494443051;N:27250,74,71,,,466613214,395400217,407881798,494443051,27250,SRX5978260,SRS4884515,SRA894667,GEO,Oxford University,2,0.95055,0.76043,0.0868,0.07313,0.75436,0.79295,0.51961,0.5131,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52775,SRR9207190,SRX5978260,SRS4884515,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq MO DN rep1,GSM3855052,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,RNA seq MO DN rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected,GSM3855052,GSM3855052: MO DN rep1; Danio rerio; RNA Seq,GSM3855052,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855052,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_247_1_pair.fq.gz WTCHG_236897_247_2_pair.fq.gz,fastq fastq,1746830974.0,11912737.0,GSM3855052 r2,0:74.80 1:71.83,A:461791276;C:389648653;G:402516938;T:492843307;N:30800,74,71,,,461791276,389648653,402516938,492843307,30800,SRX5978260,SRS4884515,SRA894667,GEO,Oxford University,2,0.94945,0.75002,0.08645,0.07146,0.75564,0.79247,0.52424,0.51007,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52776,SRR9207187,SRX5978259,SRS4884514,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep3,GSM3855051,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855051,GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq,GSM3855051,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855051,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_256_1_pair.fq.gz WTCHG_236896_256_2_pair.fq.gz,fastq fastq,2404346186.0,16361688.0,GSM3855051 r1,0:74.85 1:72.10,A:623840845;C:555338266;G:572145582;T:652983438;N:38055,74,72,,,623840845,555338266,572145582,652983438,38055,SRX5978259,SRS4884514,SRA894667,GEO,Oxford University,2,0.95156,0.77737,0.06227,0.05592,0.78013,0.80811,0.47747,0.46476,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52777,SRR9207188,SRX5978259,SRS4884514,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep3,GSM3855051,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855051,GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq,GSM3855051,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855051,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_256_1_pair.fq.gz WTCHG_236897_256_2_pair.fq.gz,fastq fastq,2376933896.0,16184470.0,GSM3855051 r2,0:74.81 1:72.05,A:616256503;C:545472678;G:562708331;T:652453993;N:42391,74,72,,,616256503,545472678,562708331,652453993,42391,SRX5978259,SRS4884514,SRA894667,GEO,Oxford University,2,0.95009,0.76216,0.06391,0.05506,0.78131,0.81051,0.48169,0.4736,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52778,SRR9207185,SRX5978258,SRS4884513,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep2,GSM3855050,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855050,GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq,GSM3855050,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855050,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_249_1_pair.fq.gz WTCHG_236896_249_2_pair.fq.gz,fastq fastq,2143701223.0,14577609.0,GSM3855050 r1,0:74.85 1:72.21,A:556710384;C:496467692;G:509166690;T:581322427;N:34030,74,72,,,556710384,496467692,509166690,581322427,34030,SRX5978258,SRS4884513,SRA894667,GEO,Oxford University,2,0.94754,0.79028,0.06346,0.05688,0.7811,0.80754,0.47106,0.45364,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52779,SRR9207186,SRX5978258,SRS4884513,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep2,GSM3855050,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855050,GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq,GSM3855050,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855050,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_249_1_pair.fq.gz WTCHG_236897_249_2_pair.fq.gz,fastq fastq,2117035142.0,14401911.0,GSM3855050 r2,0:74.82 1:72.18,A:549829321;C:487941130;G:501062541;T:578164319;N:37831,74,72,,,549829321,487941130,501062541,578164319,37831,SRX5978258,SRS4884513,SRA894667,GEO,Oxford University,2,0.9478,0.78326,0.06392,0.05622,0.78271,0.80764,0.46978,0.44622,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52780,SRR9207183,SRX5978257,SRS4884512,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep1,GSM3855049,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855049,GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq,GSM3855049,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855049,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_242_1_pair.fq.gz WTCHG_236896_242_2_pair.fq.gz,fastq fastq,2095674074.0,14243567.0,GSM3855049 r1,0:74.85 1:72.28,A:541444792;C:489580880;G:501484244;T:563130979;N:33179,74,72,,,541444792,489580880,501484244,563130979,33179,SRX5978257,SRS4884512,SRA894667,GEO,Oxford University,2,0.95275,0.80515,0.0503,0.0447,0.78827,0.81028,0.47691,0.47164,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52781,SRR9207184,SRX5978257,SRS4884512,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1hi rep1,GSM3855049,,source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,RNA seq Wt DP R1hi rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,haemogenic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected,GSM3855049,GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq,GSM3855049,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855049,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_242_1_pair.fq.gz WTCHG_236897_242_2_pair.fq.gz,fastq fastq,2063492969.0,14026048.0,GSM3855049 r2,0:74.82 1:72.30,A:533045811;C:480334040;G:492421855;T:557653783;N:37480,74,72,,,533045811,480334040,492421855,557653783,37480,SRX5978257,SRS4884512,SRA894667,GEO,Oxford University,2,0.95243,0.79788,0.04971,0.04343,0.7878,0.81016,0.48035,0.46512,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52782,SRR9207181,SRX5978256,SRS4884511,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep3,GSM3855048,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855048,GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq,GSM3855048,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_265_1_pair.fq.gz WTCHG_236896_265_2_pair.fq.gz,fastq fastq,1745443128.0,11892304.0,GSM3855048 r1,0:74.86 1:71.91,A:453150216;C:403838492;G:414952890;T:473474634;N:26896,74,71,,,453150216,403838492,414952890,473474634,26896,SRX5978256,SRS4884511,SRA894667,GEO,Oxford University,2,0.95301,0.78351,0.0658,0.06097,0.78368,0.80941,0.47251,0.4445,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52783,SRR9207182,SRX5978256,SRS4884511,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep3,GSM3855048,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855048,GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq,GSM3855048,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_265_1_pair.fq.gz WTCHG_236897_265_2_pair.fq.gz,fastq fastq,1728817726.0,11782024.0,GSM3855048 r2,0:74.82 1:71.91,A:448845759;C:398200726;G:409703125;T:472037424;N:30692,74,71,,,448845759,398200726,409703125,472037424,30692,SRX5978256,SRS4884511,SRA894667,GEO,Oxford University,2,0.9518,0.77329,0.06602,0.05955,0.78423,0.81051,0.47776,0.46478,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52784,SRR9207179,SRX5978255,SRS4884510,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep2,GSM3855047,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855047,GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq,GSM3855047,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855047,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_250_1_pair.fq.gz WTCHG_236896_250_2_pair.fq.gz,fastq fastq,2096576707.0,14262609.0,GSM3855047 r1,0:74.87 1:72.13,A:536583711;C:491572815;G:509433296;T:558953949;N:32936,74,72,,,536583711,491572815,509433296,558953949,32936,SRX5978255,SRS4884510,SRA894667,GEO,Oxford University,2,0.95719,0.76406,0.04256,0.03937,0.7989,0.82856,0.40968,0.4591,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52785,SRR9207180,SRX5978255,SRS4884510,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep2,GSM3855047,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855047,GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq,GSM3855047,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855047,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_250_1_pair.fq.gz WTCHG_236897_250_2_pair.fq.gz,fastq fastq,2081468598.0,14169082.0,GSM3855047 r2,0:74.83 1:72.07,A:532025059;C:484883611;G:503099767;T:561423564;N:36597,74,72,,,532025059,484883611,503099767,561423564,36597,SRX5978255,SRS4884510,SRA894667,GEO,Oxford University,2,0.95742,0.74712,0.04275,0.03741,0.79922,0.82866,0.40398,0.46313,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52786,SRR9207177,SRX5978254,SRS4884509,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep1,GSM3855046,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855046,GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq,GSM3855046,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855046,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_243_1_pair.fq.gz WTCHG_236896_243_2_pair.fq.gz,fastq fastq,2011950216.0,13680917.0,GSM3855046 r1,0:74.86 1:72.20,A:511635564;C:476475475;G:489688294;T:534119393;N:31490,74,72,,,511635564,476475475,489688294,534119393,31490,SRX5978254,SRS4884509,SRA894667,GEO,Oxford University,2,0.9571,0.78471,0.03658,0.03396,0.80247,0.8268,0.48025,0.46265,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52787,SRR9207178,SRX5978254,SRS4884509,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1med rep1,GSM3855046,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1med rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855046,GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq,GSM3855046,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855046,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_243_1_pair.fq.gz WTCHG_236897_243_2_pair.fq.gz,fastq fastq,1979368927.0,13461179.0,GSM3855046 r2,0:74.83 1:72.21,A:503539205;C:467446638;G:480794441;T:527553577;N:35066,74,72,,,503539205,467446638,480794441,527553577,35066,SRX5978254,SRS4884509,SRA894667,GEO,Oxford University,2,0.95558,0.78357,0.03711,0.03412,0.80318,0.82664,0.42185,0.46216,74,64,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52788,SRR9207175,SRX5978253,SRS4884508,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep3,GSM3855045,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855045,GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq,GSM3855045,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855045,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_266_1_pair.fq.gz WTCHG_236896_266_2_pair.fq.gz,fastq fastq,2022090059.0,13752247.0,GSM3855045 r1,0:74.84 1:72.20,A:529671943;C:466470156;G:476864148;T:549051395;N:32417,74,72,,,529671943,466470156,476864148,549051395,32417,SRX5978253,SRS4884508,SRA894667,GEO,Oxford University,2,0.94638,0.80375,0.07924,0.06889,0.76098,0.78636,0.4888,0.46168,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52789,SRR9207176,SRX5978253,SRS4884508,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep3,GSM3855045,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855045,GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq,GSM3855045,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855045,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_266_1_pair.fq.gz WTCHG_236897_266_2_pair.fq.gz,fastq fastq,1996491732.0,13581226.0,GSM3855045 r2,0:74.81 1:72.20,A:522970179;C:458424995;G:469211257;T:545848558;N:36743,74,72,,,522970179,458424995,469211257,545848558,36743,SRX5978253,SRS4884508,SRA894667,GEO,Oxford University,2,0.94571,0.7947,0.08062,0.06773,0.76116,0.78591,0.49549,0.46742,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52790,SRR9207173,SRX5978252,SRS4884507,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep2,GSM3855044,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855044,GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq,GSM3855044,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855044,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_251_1_pair.fq.gz WTCHG_236896_251_2_pair.fq.gz,fastq fastq,2166575163.0,14709523.0,GSM3855044 r1,0:74.86 1:72.43,A:559933570;C:510454967;G:520888591;T:575264053;N:33982,74,72,,,559933570,510454967,520888591,575264053,33982,SRX5978252,SRS4884507,SRA894667,GEO,Oxford University,2,0.95094,0.8211,0.0594,0.05292,0.76664,0.79253,0.4795,0.4638,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52791,SRR9207174,SRX5978252,SRS4884507,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep2,GSM3855044,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855044,GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq,GSM3855044,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855044,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_251_1_pair.fq.gz WTCHG_236897_251_2_pair.fq.gz,fastq fastq,2148630324.0,14593830.0,GSM3855044 r2,0:74.83 1:72.40,A:555362600;C:503529612;G:514542689;T:575156489;N:38934,74,72,,,555362600,503529612,514542689,575156489,38934,SRX5978252,SRS4884507,SRA894667,GEO,Oxford University,2,0.95053,0.81036,0.06102,0.05199,0.76897,0.79354,0.47523,0.46186,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52792,SRR9207171,SRX5978251,SRS4884506,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep1,GSM3855043,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855043,GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq,GSM3855043,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_244_1_pair.fq.gz WTCHG_236896_244_2_pair.fq.gz,fastq fastq,1899807957.0,12921335.0,GSM3855043 r1,0:74.85 1:72.17,A:494455972;C:440267035;G:451386907;T:513668319;N:29724,74,72,,,494455972,440267035,451386907,513668319,29724,SRX5978251,SRS4884506,SRA894667,GEO,Oxford University,2,0.94888,0.79567,0.06354,0.05518,0.77041,0.79837,0.48973,0.47834,75,73,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52793,SRR9207172,SRX5978251,SRS4884506,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DP R1lo rep1,GSM3855043,,source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,RNA seq Wt DP R1lo rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,aortic endothelium,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected,GSM3855043,GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq,GSM3855043,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_244_1_pair.fq.gz WTCHG_236897_244_2_pair.fq.gz,fastq fastq,1882109620.0,12807285.0,GSM3855043 r2,0:74.82 1:72.14,A:489932533;C:433346981;G:444869178;T:513927823;N:33105,74,72,,,489932533,433346981,444869178,513927823,33105,SRX5978251,SRS4884506,SRA894667,GEO,Oxford University,2,0.94837,0.78199,0.06553,0.05587,0.77068,0.79967,0.48984,0.47719,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52800,SRR9207163,SRX5978247,SRS4884502,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep3,GSM3855039,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855039,GSM3855039: Wt DN rep3; Danio rerio; RNA Seq,GSM3855039,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_267_1_pair.fq.gz WTCHG_236896_267_2_pair.fq.gz,fastq fastq,1812059909.0,12410104.0,GSM3855039 r1,0:74.81 1:71.21,A:491620609;C:383394578;G:398030819;T:538985491;N:28412,74,71,,,491620609,383394578,398030819,538985491,28412,SRX5978247,SRS4884502,SRA894667,GEO,Oxford University,2,0.93321,0.68178,0.15093,0.11867,0.75282,0.79468,0.51285,0.51101,75,74,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52801,SRR9207164,SRX5978247,SRS4884502,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep3,GSM3855039,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep3,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855039,GSM3855039: Wt DN rep3; Danio rerio; RNA Seq,GSM3855039,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_267_1_pair.fq.gz WTCHG_236897_267_2_pair.fq.gz,fastq fastq,1798726377.0,12321488.0,GSM3855039 r2,0:74.77 1:71.21,A:487870380;C:378213454;G:393167780;T:539442882;N:31881,74,71,,,487870380,378213454,393167780,539442882,31881,SRX5978247,SRS4884502,SRA894667,GEO,Oxford University,2,0.93183,0.67372,0.15009,0.11547,0.7555,0.79705,0.52465,0.50781,74,54,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52802,SRR9207161,SRX5978246,SRS4884501,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep2,GSM3855038,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855038,GSM3855038: Wt DN rep2; Danio rerio; RNA Seq,GSM3855038,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855038,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_252_1_pair.fq.gz WTCHG_236896_252_2_pair.fq.gz,fastq fastq,2146316233.0,14628161.0,GSM3855038 r1,0:74.84 1:71.88,A:566578244;C:489485503;G:504442873;T:585776104;N:33509,74,71,,,566578244,489485503,504442873,585776104,33509,SRX5978246,SRS4884501,SRA894667,GEO,Oxford University,2,0.94696,0.79752,0.10017,0.0872,0.74572,0.78165,0.50212,0.49488,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52803,SRR9207162,SRX5978246,SRS4884501,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep2,GSM3855038,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep2,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855038,GSM3855038: Wt DN rep2; Danio rerio; RNA Seq,GSM3855038,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855038,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_252_1_pair.fq.gz WTCHG_236897_252_2_pair.fq.gz,fastq fastq,2135407349.0,14569323.0,GSM3855038 r2,0:74.81 1:71.76,A:563322304;C:482982247;G:498831126;T:590234332;N:37340,74,71,,,563322304,482982247,498831126,590234332,37340,SRX5978246,SRS4884501,SRA894667,GEO,Oxford University,2,0.94623,0.77703,0.10192,0.08638,0.74582,0.78289,0.50539,0.48024,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52804,SRR9207159,SRX5978245,SRS4884500,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep1,GSM3855037,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855037,GSM3855037: Wt DN rep1; Danio rerio; RNA Seq,GSM3855037,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855037,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236896_245_2_pair.fq.gz WTCHG_236896_245_1_pair.fq.gz,fastq fastq,1719181139.0,11738270.0,GSM3855037 r1,0:74.81 1:71.65,A:459579950;C:379670678;G:392006300;T:487897820;N:26391,74,71,,,459579950,379670678,392006300,487897820,26391,SRX5978245,SRS4884500,SRA894667,GEO,Oxford University,2,0.93052,0.73058,0.11005,0.09187,0.7587,0.79375,0.50611,0.48538,75,73,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
52805,SRR9207160,SRX5978245,SRS4884500,SRP200560,PRJNA547066,RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf,GSE132259,Transcriptome Analysis,The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used  to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative  SP kdrl single positive  DP R1lo double positive runx1 low expression  DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.,parent bioproject:PRJNA546805,pubmed:31395869,,RNA seq Wt DN rep1,GSM3855037,,source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,RNA seq Wt DN rep1,Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities  trimmed where 20% of the bases were below quality score 20  and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo  Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene id   Counts Per Million  gene name  end value of each sample  log FC wt/mo  P value and FDR value.,non endothelial tissue,double transgenic embryos were collected  batches were split in half and were either injected or non injected with a runx1 morpholino,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos  were raised to 28 hpf 30 hpf.,age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected,GSM3855037,GSM3855037: Wt DN rep1; Danio rerio; RNA Seq,GSM3855037,,1,whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN  Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.,GEO Accession:GSM3855037,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP200560,,,WTCHG_236897_245_1_pair.fq.gz WTCHG_236897_245_2_pair.fq.gz,fastq fastq,1710103502.0,11683422.0,GSM3855037 r2,0:74.77 1:71.60,A:456758769;C:375069094;G:387904698;T:490340725;N:30216,74,71,,,456758769,375069094,387904698,490340725,30216,SRX5978245,SRS4884500,SRA894667,GEO,Oxford University,2,0.93089,0.71617,0.1094,0.08897,0.75879,0.79667,0.51735,0.49687,74,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2019-06-05,Pharyngula,Embryo,Endothelium,Cardiovascular System
55747,SRR10753218,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN707-S517=Aug1_Cell_49.fastq.gz run1696_lane2_read1_indexN707-S517=Aug1_Cell_49.fastq.gz,fastq fastq,283120950.0,1887473.0,GSM4230287 r1,0:75 1:75,A:78921390;C:62364350;G:62670695;T:79125765;N:38750,75,75,,,78921390,62364350,62670695,79125765,38750,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90632,0.92036,0.16158,0.16744,0.93332,0.93389,0.4857,0.48751,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55748,SRR10753219,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S502=Aug1_Cell_58.fastq.gz run1696_lane2_read1_indexN709-S502=Aug1_Cell_58.fastq.gz,fastq fastq,245846550.0,1638977.0,GSM4230287 r10,0:75 1:75,A:67896939;C:54764431;G:55135813;T:68016031;N:33336,75,75,,,67896939,54764431,55135813,68016031,33336,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90267,0.90773,0.18676,0.18997,0.92983,0.92971,0.49203,0.49454,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55749,SRR10753220,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN710-S503=Aug1_Cell_59.fastq.gz run1696_lane2_read1_indexN710-S503=Aug1_Cell_59.fastq.gz,fastq fastq,254226450.0,1694843.0,GSM4230287 r11,0:75 1:75,A:72181308;C:54619189;G:54984718;T:72405980;N:35255,75,75,,,72181308,54619189,54984718,72405980,35255,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89184,0.89943,0.33071,0.3348,0.90538,0.90514,0.54519,0.54232,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55750,SRR10753221,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S504=Aug1_Cell_60.fastq.gz run1696_lane2_read2_indexN711-S504=Aug1_Cell_60.fastq.gz,fastq fastq,272723400.0,1818156.0,GSM4230287 r12,0:75 1:75,A:75891977;C:60178887;G:60639000;T:75975500;N:38036,75,75,,,75891977,60178887,60639000,75975500,38036,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91617,0.92262,0.19662,0.20134,0.93072,0.9307,0.43264,0.43459,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55751,SRR10753222,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN712-S505=Aug1_Cell_61.fastq.gz run1696_lane2_read1_indexN712-S505=Aug1_Cell_61.fastq.gz,fastq fastq,328643250.0,2190955.0,GSM4230287 r13,0:75 1:75,A:91428860;C:72391345;G:72874053;T:91904041;N:44951,75,75,,,91428860,72391345,72874053,91904041,44951,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90728,0.91292,0.20245,0.20556,0.91701,0.91664,0.47925,0.47785,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55752,SRR10753223,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S506=Aug1_Cell_62.fastq.gz run1696_lane2_read2_indexN701-S506=Aug1_Cell_62.fastq.gz,fastq fastq,393051600.0,2620344.0,GSM4230287 r14,0:75 1:75,A:107520133;C:88489033;G:89202131;T:107788164;N:52139,75,75,,,107520133,88489033,89202131,107788164,52139,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91538,0.92003,0.14754,0.14967,0.89438,0.89572,0.48906,0.46829,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55753,SRR10753224,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S507=Aug1_Cell_63.fastq.gz run1696_lane2_read2_indexN702-S507=Aug1_Cell_63.fastq.gz,fastq fastq,266633850.0,1777559.0,GSM4230287 r15,0:75 1:75,A:75310904;C:57522159;G:58016352;T:75748192;N:36243,75,75,,,75310904,57522159,58016352,75748192,36243,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.8963,0.91004,0.26603,0.27276,0.92064,0.91993,0.49301,0.49362,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55754,SRR10753225,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S508=Aug1_Cell_64.fastq.gz run1696_lane2_read2_indexN703-S508=Aug1_Cell_64.fastq.gz,fastq fastq,320260050.0,2135067.0,GSM4230287 r16,0:75 1:75,A:88326766;C:70952312;G:71719762;T:89217755;N:43455,75,75,,,88326766,70952312,71719762,89217755,43455,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90631,0.91303,0.17305,0.1758,0.91226,0.91194,0.4751,0.47508,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55755,SRR10753226,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S517=Aug1_Cell_65.fastq.gz run1696_lane2_read1_indexN709-S517=Aug1_Cell_65.fastq.gz,fastq fastq,237092850.0,1580619.0,GSM4230287 r17,0:75 1:75,A:65593919;C:52797142;G:53078356;T:65591887;N:31546,75,75,,,65593919,52797142,53078356,65591887,31546,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9084,0.91253,0.16047,0.16296,0.91291,0.91232,0.47821,0.48265,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55756,SRR10753227,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S502=Aug1_Cell_66.fastq.gz run1696_lane2_read2_indexN710-S502=Aug1_Cell_66.fastq.gz,fastq fastq,203466600.0,1356444.0,GSM4230287 r18,0:75 1:75,A:57338640;C:43614133;G:44244871;T:58241187;N:27769,75,75,,,57338640,43614133,44244871,58241187,27769,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.88694,0.89395,0.35775,0.36017,0.93371,0.93428,0.64977,0.64812,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55757,SRR10753228,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S503=Aug1_Cell_67.fastq.gz run1696_lane2_read2_indexN711-S503=Aug1_Cell_67.fastq.gz,fastq fastq,382760100.0,2551734.0,GSM4230287 r19,0:75 1:75,A:104074844;C:86846190;G:87465046;T:104321801;N:52219,75,75,,,104074844,86846190,87465046,104321801,52219,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92294,0.92788,0.14352,0.14599,0.91845,0.91782,0.48227,0.48103,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55758,SRR10753229,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S502=Aug1_Cell_50.fastq.gz run1696_lane2_read2_indexN708-S502=Aug1_Cell_50.fastq.gz,fastq fastq,267098700.0,1780658.0,GSM4230287 r2,0:75 1:75,A:74382570;C:58775515;G:59120917;T:74783242;N:36456,75,75,,,74382570,58775515,59120917,74783242,36456,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90724,0.91983,0.2402,0.24535,0.92547,0.92533,0.45641,0.4586,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55759,SRR10753230,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S504=Aug1_Cell_68.fastq.gz run1696_lane2_read2_indexN712-S504=Aug1_Cell_68.fastq.gz,fastq fastq,318756750.0,2125045.0,GSM4230287 r20,0:75 1:75,A:87025537;C:72058246;G:72667582;T:86962614;N:42771,75,75,,,87025537,72058246,72667582,86962614,42771,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91149,0.91879,0.14134,0.14484,0.9181,0.91839,0.48713,0.48686,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55760,SRR10753231,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S505=Aug1_Cell_69.fastq.gz run1696_lane2_read2_indexN701-S505=Aug1_Cell_69.fastq.gz,fastq fastq,284858550.0,1899057.0,GSM4230287 r21,0:75 1:75,A:78978323;C:63093139;G:63404944;T:79343904;N:38240,75,75,,,78978323,63093139,63404944,79343904,38240,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91426,0.92025,0.1863,0.18952,0.92855,0.92849,0.50311,0.50162,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55761,SRR10753232,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S506=Aug1_Cell_70.fastq.gz run1696_lane2_read2_indexN702-S506=Aug1_Cell_70.fastq.gz,fastq fastq,284898300.0,1899322.0,GSM4230287 r22,0:75 1:75,A:78397302;C:63504322;G:64181815;T:78775032;N:39829,75,75,,,78397302,63504322,64181815,78775032,39829,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90463,0.9098,0.13564,0.137,0.90382,0.90461,0.48397,0.4914,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55762,SRR10753233,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S507=Aug1_Cell_71.fastq.gz run1696_lane2_read2_indexN703-S507=Aug1_Cell_71.fastq.gz,fastq fastq,320753850.0,2138359.0,GSM4230287 r23,0:75 1:75,A:88975252;C:70589715;G:71455216;T:89691991;N:41676,75,75,,,88975252,70589715,71455216,89691991,41676,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.87801,0.88372,0.22781,0.23132,0.9036,0.90408,0.47968,0.48892,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55763,SRR10753234,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S508=Aug1_Cell_72.fastq.gz run1696_lane2_read2_indexN704-S508=Aug1_Cell_72.fastq.gz,fastq fastq,299361600.0,1995744.0,GSM4230287 r24,0:75 1:75,A:79430814;C:70183806;G:70603054;T:79102903;N:41023,75,75,,,79430814,70183806,70603054,79102903,41023,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90697,0.91051,0.13467,0.13564,0.92669,0.92691,0.44358,0.43646,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55764,SRR10753235,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S517=Aug1_Cell_73.fastq.gz run1696_lane2_read2_indexN710-S517=Aug1_Cell_73.fastq.gz,fastq fastq,177953400.0,1186356.0,GSM4230287 r25,0:75 1:75,A:50000069;C:38723482;G:38933711;T:50273254;N:22884,75,75,,,50000069,38723482,38933711,50273254,22884,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90193,0.91597,0.18328,0.18867,0.95063,0.95028,0.47314,0.47044,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55765,SRR10753236,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S502=Aug1_Cell_74.fastq.gz run1696_lane2_read2_indexN711-S502=Aug1_Cell_74.fastq.gz,fastq fastq,279180300.0,1861202.0,GSM4230287 r26,0:75 1:75,A:78643117;C:60355928;G:60826366;T:79317071;N:37818,75,75,,,78643117,60355928,60826366,79317071,37818,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9052,0.90984,0.27142,0.27375,0.96867,0.96865,0.51907,0.52285,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55766,SRR10753237,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S503=Aug1_Cell_75.fastq.gz run1696_lane2_read2_indexN712-S503=Aug1_Cell_75.fastq.gz,fastq fastq,349436850.0,2329579.0,GSM4230287 r27,0:75 1:75,A:97251265;C:76806628;G:77656677;T:97675062;N:47218,75,75,,,97251265,76806628,77656677,97675062,47218,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90399,0.90953,0.22592,0.22897,0.90962,0.91015,0.48568,0.48353,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55767,SRR10753238,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S504=Aug1_Cell_76.fastq.gz run1696_lane2_read2_indexN701-S504=Aug1_Cell_76.fastq.gz,fastq fastq,287349300.0,1915662.0,GSM4230287 r28,0:75 1:75,A:79830728;C:63683589;G:64040532;T:79755658;N:38793,75,75,,,79830728,63683589,64040532,79755658,38793,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91249,0.91836,0.18353,0.18679,0.91942,0.91918,0.48879,0.48925,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55768,SRR10753239,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S505=Aug1_Cell_77.fastq.gz run1696_lane2_read2_indexN702-S505=Aug1_Cell_77.fastq.gz,fastq fastq,288709800.0,1924732.0,GSM4230287 r29,0:75 1:75,A:79556851;C:64127745;G:64891546;T:80093515;N:40143,75,75,,,79556851,64127745,64891546,80093515,40143,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90821,0.91323,0.185,0.18708,0.89018,0.89057,0.48437,0.48334,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55769,SRR10753240,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S503=Aug1_Cell_51.fastq.gz run1696_lane2_read2_indexN709-S503=Aug1_Cell_51.fastq.gz,fastq fastq,241206600.0,1608044.0,GSM4230287 r3,0:75 1:75,A:66846250;C:53388095;G:53773714;T:67165505;N:33036,75,75,,,66846250,53388095,53773714,67165505,33036,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90761,0.91183,0.20482,0.2069,0.91437,0.91435,0.50196,0.50907,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55770,SRR10753241,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S506=Aug1_Cell_78.fastq.gz run1696_lane2_read2_indexN703-S506=Aug1_Cell_78.fastq.gz,fastq fastq,350680950.0,2337873.0,GSM4230287 r30,0:75 1:75,A:97180433;C:77760723;G:78449256;T:97242648;N:47890,75,75,,,97180433,77760723,78449256,97242648,47890,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91178,0.9175,0.18486,0.1874,0.91463,0.91612,0.51946,0.52606,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55771,SRR10753242,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S507=Aug1_Cell_79.fastq.gz run1696_lane2_read2_indexN704-S507=Aug1_Cell_79.fastq.gz,fastq fastq,301610700.0,2010738.0,GSM4230287 r31,0:75 1:75,A:83008152;C:67488146;G:68027086;T:83048256;N:39060,75,75,,,83008152,67488146,68027086,83048256,39060,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90738,0.92127,0.1374,0.14115,0.90281,0.90323,0.49906,0.5053,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55772,SRR10753243,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S508=Aug1_Cell_80.fastq.gz run1696_lane2_read2_indexN705-S508=Aug1_Cell_80.fastq.gz,fastq fastq,376354800.0,2509032.0,GSM4230287 r32,0:75 1:75,A:103364840;C:83901867;G:84865220;T:104170582;N:52291,75,75,,,103364840,83901867,84865220,104170582,52291,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9055,0.91077,0.15298,0.1558,0.89116,0.89167,0.48355,0.48618,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55773,SRR10753244,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S517=Aug1_Cell_81.fastq.gz run1696_lane2_read2_indexN711-S517=Aug1_Cell_81.fastq.gz,fastq fastq,299770350.0,1998469.0,GSM4230287 r33,0:75 1:75,A:82289754;C:67187388;G:67586885;T:82664262;N:42061,75,75,,,82289754,67187388,67586885,82664262,42061,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91515,0.92029,0.16415,0.16637,0.93576,0.9357,0.45125,0.44424,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55774,SRR10753245,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S502=Aug1_Cell_82.fastq.gz run1696_lane2_read2_indexN712-S502=Aug1_Cell_82.fastq.gz,fastq fastq,324078300.0,2160522.0,GSM4230287 r34,0:75 1:75,A:88656173;C:73899158;G:74013418;T:87465839;N:43712,75,75,,,88656173,73899158,74013418,87465839,43712,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91408,0.91846,0.24394,0.246,0.96112,0.961,0.4816,0.59275,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55775,SRR10753246,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S503=Aug1_Cell_83.fastq.gz run1696_lane2_read2_indexN701-S503=Aug1_Cell_83.fastq.gz,fastq fastq,217032750.0,1446885.0,GSM4230287 r35,0:75 1:75,A:59534071;C:48070176;G:49062629;T:60336044;N:29830,75,75,,,59534071,48070176,49062629,60336044,29830,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.87055,0.87748,0.24417,0.24556,0.93943,0.93935,0.7874,0.78699,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55776,SRR10753247,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S504=Aug1_Cell_84.fastq.gz run1696_lane2_read2_indexN702-S504=Aug1_Cell_84.fastq.gz,fastq fastq,288801450.0,1925343.0,GSM4230287 r36,0:75 1:75,A:80110712;C:64112359;G:64456856;T:80083340;N:38183,75,75,,,80110712,64112359,64456856,80083340,38183,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91114,0.91718,0.16956,0.17377,0.91411,0.91429,0.50676,0.50753,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55777,SRR10753248,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S505=Aug1_Cell_85.fastq.gz run1696_lane2_read2_indexN703-S505=Aug1_Cell_85.fastq.gz,fastq fastq,296308500.0,1975390.0,GSM4230287 r37,0:75 1:75,A:82776201;C:64434147;G:65242392;T:83815687;N:40073,75,75,,,82776201,64434147,65242392,83815687,40073,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89013,0.89653,0.18828,0.19101,0.88787,0.88785,0.49705,0.505,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55778,SRR10753249,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S506=Aug1_Cell_86.fastq.gz run1696_lane2_read2_indexN704-S506=Aug1_Cell_86.fastq.gz,fastq fastq,329897850.0,2199319.0,GSM4230287 r38,0:75 1:75,A:91441750;C:72960353;G:73464989;T:91986497;N:44261,75,75,,,91441750,72960353,73464989,91986497,44261,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91815,0.92369,0.18544,0.18829,0.94527,0.94552,0.4292,0.43583,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55779,SRR10753250,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S507=Aug1_Cell_87.fastq.gz run1696_lane2_read2_indexN705-S507=Aug1_Cell_87.fastq.gz,fastq fastq,322963500.0,2153090.0,GSM4230287 r39,0:75 1:75,A:88789292;C:72352695;G:72843334;T:88935120;N:43059,75,75,,,88789292,72352695,72843334,88935120,43059,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92095,0.92789,0.14339,0.14586,0.94308,0.94359,0.49931,0.4992,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55780,SRR10753251,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S504=Aug1_Cell_52.fastq.gz run1696_lane2_read2_indexN710-S504=Aug1_Cell_52.fastq.gz,fastq fastq,265346250.0,1768975.0,GSM4230287 r4,0:75 1:75,A:74074058;C:58293208;G:58627997;T:74316626;N:34361,75,75,,,74074058,58293208,58627997,74316626,34361,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90624,0.9193,0.21417,0.22055,0.90948,0.90938,0.49135,0.48435,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55781,SRR10753252,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S508=Aug1_Cell_88.fastq.gz run1696_lane2_read2_indexN706-S508=Aug1_Cell_88.fastq.gz,fastq fastq,346084350.0,2307229.0,GSM4230287 r40,0:75 1:75,A:95282196;C:77387933;G:77889452;T:95477032;N:47737,75,75,,,95282196,77387933,77889452,95477032,47737,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91441,0.91887,0.14069,0.14283,0.91589,0.91589,0.48567,0.48486,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55782,SRR10753253,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S517=Aug1_Cell_89.fastq.gz run1696_lane2_read2_indexN712-S517=Aug1_Cell_89.fastq.gz,fastq fastq,299214150.0,1994761.0,GSM4230287 r41,0:75 1:75,A:84760328;C:64330889;G:64713377;T:85368909;N:40647,75,75,,,84760328,64330889,64713377,85368909,40647,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89925,0.9046,0.23324,0.23787,0.93754,0.93787,0.49809,0.49658,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55783,SRR10753254,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S502=Aug1_Cell_90.fastq.gz run1696_lane2_read2_indexN701-S502=Aug1_Cell_90.fastq.gz,fastq fastq,296379750.0,1975865.0,GSM4230287 r42,0:75 1:75,A:84724008;C:64477005;G:63594204;T:83543595;N:40938,75,75,,,84724008,64477005,63594204,83543595,40938,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91759,0.92318,0.59672,0.60102,0.9489,0.94884,0.51902,0.51562,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55784,SRR10753255,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S503=Aug1_Cell_91.fastq.gz run1696_lane2_read2_indexN702-S503=Aug1_Cell_91.fastq.gz,fastq fastq,381532350.0,2543549.0,GSM4230287 r43,0:75 1:75,A:104927348;C:85478286;G:86116958;T:104958903;N:50855,75,75,,,104927348,85478286,86116958,104958903,50855,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90434,0.90948,0.21281,0.2161,0.90609,0.90652,0.48698,0.48654,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55785,SRR10753256,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S504=Aug1_Cell_92.fastq.gz run1696_lane2_read2_indexN703-S504=Aug1_Cell_92.fastq.gz,fastq fastq,277685850.0,1851239.0,GSM4230287 r44,0:75 1:75,A:77163713;C:61411043;G:61889515;T:77184100;N:37479,75,75,,,77163713,61411043,61889515,77184100,37479,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89942,0.90575,0.19557,0.19955,0.92514,0.92659,0.50956,0.51364,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55786,SRR10753257,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S505=Aug1_Cell_93.fastq.gz run1696_lane2_read2_indexN704-S505=Aug1_Cell_93.fastq.gz,fastq fastq,287073450.0,1913823.0,GSM4230287 r45,0:75 1:75,A:80239990;C:62929136;G:63425774;T:80441246;N:37304,75,75,,,80239990,62929136,63425774,80441246,37304,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90019,0.91389,0.16561,0.16949,0.90946,0.9092,0.44449,0.49777,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55787,SRR10753258,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S506=Aug1_Cell_94.fastq.gz run1696_lane2_read2_indexN705-S506=Aug1_Cell_94.fastq.gz,fastq fastq,285636450.0,1904243.0,GSM4230287 r46,0:75 1:75,A:80380364;C:61727196;G:62532553;T:80957412;N:38925,75,75,,,80380364,61727196,62532553,80957412,38925,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.88701,0.89489,0.28158,0.28356,0.9391,0.94026,0.62885,0.62711,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55788,SRR10753259,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S507=Aug1_Cell_95.fastq.gz run1696_lane2_read2_indexN706-S507=Aug1_Cell_95.fastq.gz,fastq fastq,319043700.0,2126958.0,GSM4230287 r47,0:75 1:75,A:88834179;C:69902391;G:70666753;T:89598537;N:41840,75,75,,,88834179,69902391,70666753,89598537,41840,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90283,0.90836,0.21154,0.21543,0.91082,0.91143,0.49488,0.48046,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55789,SRR10753260,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S508=Aug1_Cell_96.fastq.gz run1696_lane2_read2_indexN707-S508=Aug1_Cell_96.fastq.gz,fastq fastq,23619300.0,157462.0,GSM4230287 r48,0:75 1:75,A:6648282;C:5444230;G:4975645;T:6548172;N:2971,75,75,,,6648282,5444230,4975645,6548172,2971,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.72054,0.86233,0.11482,0.14219,0.95556,0.95627,0.46808,0.46497,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55790,SRR10753261,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S505=Aug1_Cell_53.fastq.gz run1696_lane2_read2_indexN711-S505=Aug1_Cell_53.fastq.gz,fastq fastq,306382800.0,2042552.0,GSM4230287 r5,0:75 1:75,A:86067136;C:66550597;G:67047629;T:86675235;N:42203,75,75,,,86067136,66550597,67047629,86675235,42203,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90104,0.90602,0.25949,0.26321,0.94073,0.94091,0.51681,0.46212,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55791,SRR10753262,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S506=Aug1_Cell_54.fastq.gz run1696_lane2_read2_indexN712-S506=Aug1_Cell_54.fastq.gz,fastq fastq,351081900.0,2340546.0,GSM4230287 r6,0:75 1:75,A:98081793;C:77038508;G:77373196;T:98539502;N:48901,75,75,,,98081793,77038508,77373196,98539502,48901,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90946,0.91275,0.18599,0.18944,0.91995,0.92064,0.51022,0.51557,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55792,SRR10753263,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S507=Aug1_Cell_55.fastq.gz run1696_lane2_read2_indexN701-S507=Aug1_Cell_55.fastq.gz,fastq fastq,313116300.0,2087442.0,GSM4230287 r7,0:75 1:75,A:88330056;C:67596816;G:68042817;T:89103852;N:42759,75,75,,,88330056,67596816,68042817,89103852,42759,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89433,0.89911,0.27071,0.27406,0.90234,0.9025,0.49714,0.49217,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55793,SRR10753264,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S508=Aug1_Cell_56.fastq.gz run1696_lane2_read2_indexN702-S508=Aug1_Cell_56.fastq.gz,fastq fastq,337006050.0,2246707.0,GSM4230287 r8,0:75 1:75,A:91946919;C:76067774;G:76661595;T:92284491;N:45271,75,75,,,91946919,76067774,76661595,92284491,45271,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.921,0.92486,0.10214,0.10415,0.89528,0.89591,0.4974,0.48846,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55794,SRR10753265,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S517=Aug1_Cell_57.fastq.gz run1696_lane2_read2_indexN708-S517=Aug1_Cell_57.fastq.gz,fastq fastq,264639450.0,1764263.0,GSM4230287 r9,0:75 1:75,A:74195564;C:57388120;G:58187904;T:74832787;N:35075,75,75,,,74195564,57388120,58187904,74832787,35075,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89601,0.9097,0.3037,0.31018,0.92133,0.92028,0.52888,0.54457,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55795,SRR10753170,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN701-S517=Jul11_Cell_1.fastq.gz run1696_lane2_read1_indexN701-S517=Jul11_Cell_1.fastq.gz,fastq fastq,234610050.0,1564067.0,GSM4230286 r1,0:75 1:75,A:65886611;C:50927760;G:51256089;T:66507455;N:32135,75,75,,,65886611,50927760,51256089,66507455,32135,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90542,0.91089,0.2189,0.22149,0.88373,0.88394,0.4997,0.50524,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55796,SRR10753171,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S502=Jul11_Cell_10.fastq.gz run1696_lane2_read2_indexN703-S502=Jul11_Cell_10.fastq.gz,fastq fastq,229833900.0,1532226.0,GSM4230286 r10,0:75 1:75,A:64620859;C:49968774;G:50168025;T:65045353;N:30889,75,75,,,64620859,49968774,50168025,65045353,30889,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90987,0.91683,0.23924,0.24284,0.93663,0.9373,0.51987,0.51778,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55797,SRR10753172,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S503=Jul11_Cell_11.fastq.gz run1696_lane2_read2_indexN704-S503=Jul11_Cell_11.fastq.gz,fastq fastq,263149800.0,1754332.0,GSM4230286 r11,0:75 1:75,A:73836706;C:57360247;G:57722644;T:74193453;N:36750,75,75,,,73836706,57360247,57722644,74193453,36750,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89945,0.90639,0.23998,0.24336,0.91133,0.91086,0.51231,0.51605,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System