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272 rows where experiment.library_layout = "PAIRED", tissue_curation = "Endothelium" and tissue_curation_coarse = "Cardiovascular System"

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technology 6

devstage_curation 6

experiment.library_selection 3

devstage_curation_coarse 3

experiment.library_source 2

tissue_curation_coarse 1

  • Cardiovascular System · 272 ✖

tissue_curation 1

  • Endothelium · 272 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_layout 1

  • PAIRED · 272 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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
50604 50604 SRR8169175 SRX4989831 SRS4025849 SRP168005 PRJNA504385 Endothelial transcriptome of 1dpf Zebrafish empryo PRJNA504385 Other The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.       Endothelial cells EC   strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Endothelium|cell type:Endothelial|BioSampleModel:Model organism or animal                 Endothelial cells EC EC PolyA RNA Seq     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP168005     EC_R1.fastq EC_R2.fastq fastq fastq 3373890496.0 22196648.0 EC R1.fastq 0:76 1:76 A:984631808;C:769706826;G:812424195;T:790813473;N:16314194 76 76     984631808 769706826 812424195 790813473 16314194 SRX4989831 SRS4025849 SRA805845 CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center CSIR-Institute of Genomics and Integrative Biology 2 0.92323 0.92543 0.07989 0.0849 0.76842 0.77964 0.46181 0.47429 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   India 2019-12-06 Pharyngula Embryo Endothelium Cardiovascular System
50605 50605 SRR8169176 SRX4989830 SRS4025850 SRP168005 PRJNA504385 Endothelial transcriptome of 1dpf Zebrafish empryo PRJNA504385 Other The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.       Non endothelial cells NEC   strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Whole organism devoid of endothelium|BioSampleModel:Model organism or animal                 Non endothelial cells NEC NEC PolyA RNA Seq     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP168005     NEC_R2.fastq NEC_R1.fastq fastq fastq 3903685432.0 25682141.0 NEC R1.fastq 0:76 1:76 A:1078599801;C:913868400;G:942281029;T:950473482;N:18462720 76 76     1078599801 913868400 942281029 950473482 18462720 SRX4989830 SRS4025850 SRA805845 CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center CSIR-Institute of Genomics and Integrative Biology 2 0.93037 0.92641 0.10373 0.11231 0.72644 0.74081 0.48329 0.48409 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   India 2019-12-06 Pharyngula Embryo Endothelium Cardiovascular System
52764 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
55379 55379 SRR10323881 SRX7034716 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 10 10 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 3356658750.0 22377725.0 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:875300673;C:782517555;G:796855605;T:901672776;N:312141 75 75     875300673 782517555 796855605 901672776 312141 SRX7034716 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.68437 0.73326 0.04743 0.05194 0.80241 0.80517 0.51875 0.52196 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55380 55380 SRR10323882 SRX7034715 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 9 9 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz fastq fastq 3459242400.0 23061616.0 RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:924400584;C:762078140;G:779330250;T:993109509;N:323917 75 75     924400584 762078140 779330250 993109509 323917 SRX7034715 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.67032 0.73764 0.07629 0.08303 0.80856 0.80748 0.52094 0.52695 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55381 55381 SRR10323883 SRX7034714 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 8 8 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 3238312500.0 21588750.0 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:881635390;C:656958401;G:673596788;T:1025824968;N:296953 75 75     881635390 656958401 673596788 1025824968 296953 SRX7034714 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.59623 0.72377 0.07781 0.08944 0.80608 0.8016 0.53277 0.53095 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55382 55382 SRR10323884 SRX7034713 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 7 7 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3255021150.0 21700141.0 RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:858912760;C:733048670;G:750496371;T:912263495;N:299854 75 75     858912760 733048670 750496371 912263495 299854 SRX7034713 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.65481 0.71883 0.05477 0.05995 0.7903 0.7921 0.51367 0.51188 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55383 55383 SRR10323885 SRX7034712 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 6 6 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2413394850.0 16089299.0 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:660807483;C:490677840;G:505039519;T:756646234;N:223774 75 75     660807483 490677840 505039519 756646234 223774 SRX7034712 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.60009 0.72319 0.09185 0.10528 0.82175 0.81815 0.5234 0.51725 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55384 55384 SRR10323886 SRX7034711 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 5 5 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3124357200.0 20829048.0 RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:844721216;C:673572690;G:689308705;T:916479849;N:274740 75 75     844721216 673572690 689308705 916479849 274740 SRX7034711 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66396 0.73861 0.09392 0.10351 0.80856 0.80797 0.53225 0.5369 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55385 55385 SRR10323891 SRX7034706 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 4 4 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2812593000.0 18750620.0 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:759189725;C:611361876;G:625876145;T:815905469;N:259785 75 75     759189725 611361876 625876145 815905469 259785 SRX7034706 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.63609 0.70403 0.08285 0.0932 0.79847 0.79959 0.52487 0.52941 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55386 55386 SRR10323898 SRX7034699 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 24 24 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 5849571450.0 38997143.0 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1574421853;C:1316832574;G:1315527058;T:1642305644;N:484321 75 75     1574421853 1316832574 1315527058 1642305644 484321 SRX7034699 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.78221 0.84034 0.0684 0.07089 0.76607 0.77025 0.50712 0.50772 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55387 55387 SRR10323899 SRX7034698 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 23 23 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 5656815000.0 37712100.0 RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116 75 75     1487198866 1332723090 1275197163 1514410765 47285116 SRX7034698 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.86399 0.76012 0.0587 0.05779 0.76461 0.9105 0.49754 0.51037 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55388 55388 SRR10323900 SRX7034697 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 22 22 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 5978780250.0 39858535.0 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259 75 75     1580804547 1404640964 1399714637 1593586843 33259 SRX7034697 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92216 0.92477 0.04155 0.04126 0.74537 0.7512 0.48148 0.49049 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55389 55389 SRR10323901 SRX7034696 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 21 21 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 8777730900.0 58518206.0 RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:2331650285;C:2053244561;G:2042022053;T:2350762388;N:51613 75 75     2331650285 2053244561 2042022053 2350762388 51613 SRX7034696 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92143 0.92455 0.04604 0.04567 0.73361 0.73923 0.4802 0.48613 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55390 55390 SRR10323902 SRX7034695 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 3 3 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3613041150.0 24086941.0 RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:972417798;C:795483066;G:808300399;T:1036510724;N:329163 75 75     972417798 795483066 808300399 1036510724 329163 SRX7034695 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66853 0.7231 0.08329 0.0907 0.78953 0.79131 0.51481 0.52637 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55391 55391 SRR10323903 SRX7034694 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 20 20 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 7211828100.0 48078854.0 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1904350731;C:1693709371;G:1687946675;T:1925778331;N:42992 75 75     1904350731 1693709371 1687946675 1925778331 42992 SRX7034694 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91819 0.92224 0.03958 0.03841 0.75584 0.76161 0.46923 0.46415 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55392 55392 SRR10323904 SRX7034693 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for VPA treatment in hemogenic endothelial cell 26hpf replicate 1 19 19 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 8021297850.0 53475319.0 RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:2121666298;C:1880005094;G:1872358379;T:2147221627;N:46452 75 75     2121666298 1880005094 1872358379 2147221627 46452 SRX7034693 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91273 0.91897 0.0437 0.04345 0.75485 0.76037 0.46259 0.47199 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55393 55393 SRR10323905 SRX7034692 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 18 18 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 4925792850.0 32838619.0 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349 75 75     1327496924 1143172265 1121827107 1332765205 531349 SRX7034692 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.9235 0.923 0.07189 0.07157 0.74576 0.7486 0.46424 0.46997 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55394 55394 SRR10323906 SRX7034691 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 17 17 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 4481194200.0 29874628.0 RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323 75 75     1207561849 1040055195 1022613796 1210492037 471323 SRX7034691 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92094 0.92157 0.07292 0.07281 0.74704 0.75067 0.47205 0.47416 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55395 55395 SRR10323907 SRX7034690 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 16 16 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz fastq fastq 2071385250.0 13809235.0 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:497024628;C:535934066;G:538798491;T:499539772;N:88293 75 75     497024628 535934066 538798491 499539772 88293 SRX7034690 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92507 0.92563 0.0745 0.07106 0.74148 0.74186 0.5137 0.52923 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55396 55396 SRR10323908 SRX7034689 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 15 15 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 1708336800.0 11388912.0 RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:413739883;C:438115098;G:440441368;T:415968029;N:72422 75 75     413739883 438115098 440441368 415968029 72422 SRX7034689 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.92948 0.93123 0.08112 0.07757 0.7472 0.74921 0.49384 0.502 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55397 55397 SRR10323909 SRX7034688 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 14 14 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 2742841800.0 18285612.0 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:771268784;C:600759252;G:605972112;T:764554978;N:286674 75 75     771268784 600759252 605972112 764554978 286674 SRX7034688 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91195 0.91276 0.15552 0.15531 0.7191 0.7247 0.487 0.47379 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55398 55398 SRR10323910 SRX7034687 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 13 13 TruSeq stranded mRNA     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 1909021350.0 12726809.0 RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:536542827;C:420010389;G:423642042;T:528630203;N:195889 75 75     536542827 420010389 423642042 528630203 195889 SRX7034687 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.91535 0.91534 0.11578 0.11457 0.73705 0.74373 0.47609 0.47115 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55399 55399 SRR10323911 SRX7034686 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 12 12 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 5135290500.0 34235270.0 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910 75 75     1339180940 1202946694 1230552771 1362120185 489910 SRX7034686 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.66031 0.70687 0.04575 0.04896 0.81075 0.81195 0.50951 0.47552 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55400 55400 SRR10323912 SRX7034685 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 11 11 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 3890046300.0 25933642.0 RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193 75 75     1020376762 903218301 916043426 1050047618 360193 SRX7034685 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.70733 0.75223 0.05929 0.06271 0.80807 0.81071 0.48475 0.49323 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55401 55401 SRR10323913 SRX7034684 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 2 2 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz fastq fastq 2547796350.0 16985309.0 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz 0:75 1:75 A:686259539;C:560800822;G:567842650;T:732652800;N:240539 75 75     686259539 560800822 567842650 732652800 240539 SRX7034684 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.70188 0.75886 0.08072 0.08833 0.8034 0.80649 0.51507 0.5194 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55402 55402 SRR10323914 SRX7034683 SRS5554730 SRP226614 PRJNA578896 Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence PRJNA578896 Other In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.         danRer10 raw data   strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal                 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 1 1 NEBNext Low Input RNA Library Prep Kit     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 3000   SRP226614     RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz fastq fastq 2438070600.0 16253804.0 RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz 0:75 1:75 A:654282012;C:534555119;G:543878428;T:705130425;N:224616 75 75     654282012 534555119 543878428 705130425 224616 SRX7034683 SRS5554730 SRA983011 Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany 2 0.69336 0.75626 0.09168 0.09896 0.80166 0.80253 0.51795 0.52538 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2019-10-24 Pharyngula Embryo Endothelium Cardiovascular System
55747 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;