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
10163,ERR5714657,ERX5430029,ERS6251768,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,WT,SAMEA8567093,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567093|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:WT|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:head kidney|sample name:E MTAB 10360:WT|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:WT p,WT p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,WT.bam,bam,1041394032.0,18596322.0,E MTAB 10360:WT,0:56,A:284652376;C:244349479;G:255850754;T:255536179;N:1005244,56,,,,284652376,244349479,255850754,255536179,1005244,ERX5430029,ERS6251768,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.9192,,0.10547,,0.84782,,0.53778,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10164,ERR5714656,ERX5430028,ERS6251767,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Rb,SAMEA8567092,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567092|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Rb|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1rb4bp|organism part:head kidney|sample name:E MTAB 10360:Rb|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Rb p,Rb p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1rb4bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Rb.bam,bam,1069920824.0,19105729.0,E MTAB 10360:Rb,0:56,A:299856824;C:238947539;G:256649537;T:273433744;N:1033180,56,,,,299856824,238947539,256649537,273433744,1033180,ERX5430028,ERS6251767,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.94145,,0.11133,,0.83191,,0.52892,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10165,ERR5714655,ERX5430027,ERS6251766,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Ra,SAMEA8567091,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567091|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Ra|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1ra5bp|organism part:head kidney|sample name:E MTAB 10360:Ra|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Ra p,Ra p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1ra5bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Ra.bam,bam,1009240400.0,18022150.0,E MTAB 10360:Ra,0:56,A:279849736;C:230130588;G:247312130;T:250994600;N:953346,56,,,,279849736,230130588,247312130,250994600,953346,ERX5430027,ERS6251766,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.95705,,0.10915,,0.84788,,0.47011,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10176,ERR5858457,ERX5504346,ERS6343450,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Naive,SAMEA8658904,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Naive p,Naive p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Naive.bam,bam,44972162730.0,499690697.0,E MTAB 10390:Naive,0:90,A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100,90,,,,13658826375,8733304343,9348137569,13228064343,3830100,ERX5504346,ERS6343450,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.89428,,0.32693,,0.75276,,0.5314,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
11753,ERR11758614,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz,fastq fastq,226833768.0,1800268.0,E MTAB 13196:FliTp124hpf S25 L001,0:28 1:98,A:65319978;C:50920193;G:49999849;T:60474280;N:119468,28,98,,,65319978,50920193,49999849,60474280,119468,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00122,0.88236,0.00056,0.09684,0.9978,0.89309,0.424,0.44186,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11754,ERR11758619,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz,fastq fastq,261098334.0,2072209.0,E MTAB 13196:FliTp124hpf S27 L001,0:28 1:98,A:76098436;C:58031830;G:57099955;T:69729759;N:138354,28,98,,,76098436,58031830,57099955,69729759,138354,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00109,0.87641,0.00062,0.0976,0.99837,0.90065,0.45555,0.48712,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11755,ERR11758589,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz,fastq fastq,1168367130.0,9272755.0,E MTAB 13196:FliTp124hpf S16 L005,0:28 1:98,A:323651598;C:269884286;G:268030176;T:306695030;N:106040,28,98,,,323651598,269884286,268030176,306695030,106040,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00491,0.90853,0.00131,0.07851,0.99019,0.84331,0.41536,0.48076,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11756,ERR11758638,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz,fastq fastq,864786636.0,6863386.0,E MTAB 13196:FliTp124hpf S22 L001,0:28 1:98,A:241767760;C:198370882;G:198049093;T:226508751;N:90150,28,98,,,241767760,198370882,198049093,226508751,90150,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00375,0.89002,0.00114,0.0769,0.99237,0.84563,0.41796,0.48995,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11757,ERR11758599,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz,fastq fastq,1795799502.0,14252377.0,E MTAB 13196:FliTp124hpf S15 L005,0:28 1:98,A:500590460;C:413239086;G:410401125;T:471402890;N:165941,28,98,,,500590460,413239086,410401125,471402890,165941,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00492,0.91242,0.0012,0.08044,0.99007,0.84668,0.42778,0.49291,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11758,ERR11758601,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz,fastq fastq,266141358.0,2112233.0,E MTAB 13196:FliTp124hpf S26 L001,0:28 1:98,A:76996100;C:59592346;G:58963461;T:70457732;N:131719,28,98,,,76996100,59592346,58963461,70457732,131719,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00106,0.88422,0.00046,0.09358,0.99782,0.89449,0.47826,0.48948,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11759,ERR11758630,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz,fastq fastq,1812847428.0,14387678.0,E MTAB 13196:FliTp124hpf S14 L005,0:28 1:98,A:502956890;C:417865079;G:416595454;T:475266679;N:163326,28,98,,,502956890,417865079,416595454,475266679,163326,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00483,0.91317,0.00123,0.07918,0.99036,0.84143,0.40704,0.4819,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11760,ERR11758603,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz,fastq fastq,1544281830.0,12256205.0,E MTAB 13196:FliTp124hpf S13 L005,0:28 1:98,A:428008915;C:356252081;G:354333187;T:405545992;N:141655,28,98,,,428008915,356252081,354333187,405545992,141655,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00507,0.91025,0.00138,0.07858,0.98987,0.84295,0.41793,0.4891,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11761,ERR11758613,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz,fastq fastq,761441436.0,6043186.0,E MTAB 13196:FliTp124hpf S21 L001,0:28 1:98,A:212876877;C:174700212;G:174244892;T:199537401;N:82054,28,98,,,212876877,174700212,174244892,199537401,82054,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00334,0.88899,0.00106,0.07762,0.99322,0.84476,0.42792,0.48783,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11762,ERR11758645,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz,fastq fastq,873938772.0,6936022.0,E MTAB 13196:FliTp124hpf S23 L001,0:28 1:98,A:245075115;C:199879929;G:199312177;T:229576663;N:94888,28,98,,,245075115,199879929,199312177,229576663,94888,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00361,0.88671,0.00104,0.07855,0.99255,0.84723,0.41141,0.4885,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11763,ERR11758598,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz,fastq fastq,164465532.0,1305282.0,E MTAB 13196:FliTp124hpf S28 L001,0:28 1:98,A:47319366;C:37063279;G:36394680;T:43602586;N:85621,28,98,,,47319366,37063279,36394680,43602586,85621,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00117,0.88222,0.00058,0.09358,0.99799,0.89217,0.54867,0.48545,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11764,ERR11758593,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz,fastq fastq,558365976.0,4431476.0,E MTAB 13196:FliTp124hpf S24 L001,0:28 1:98,A:156054630;C:128109738;G:127885708;T:146256146;N:59754,28,98,,,156054630,128109738,127885708,146256146,59754,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00345,0.8879,0.00104,0.07718,0.99322,0.84364,0.38266,0.49193,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11765,ERR11758635,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz,fastq fastq,1144014102.0,9079477.0,E MTAB 13196:Etv2Kaede WT S6 L001,0:28 1:98,A:316366230;C:260322813;G:259447166;T:307680623;N:197270,28,98,,,316366230,260322813,259447166,307680623,197270,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00336,0.89267,0.00137,0.13734,0.99545,0.81957,0.3734,0.53458,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11766,ERR11758622,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz,fastq fastq,919270926.0,7295801.0,E MTAB 13196:Etv2Kaede WT S8 L001,0:28 1:98,A:259787542;C:207541571;G:206711907;T:245072713;N:157193,28,98,,,259787542,207541571,206711907,245072713,157193,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00358,0.88757,0.00137,0.15368,0.99551,0.83378,0.36405,0.53733,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11767,ERR11758644,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz,fastq fastq,877658166.0,6965541.0,E MTAB 13196:Etv2Kaede WT S5 L001,0:28 1:98,A:243057461;C:199464116;G:198654377;T:236322700;N:159512,28,98,,,243057461,199464116,198654377,236322700,159512,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00328,0.88916,0.00127,0.13782,0.99559,0.81925,0.38227,0.53623,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11768,ERR11758628,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz,fastq fastq,930443598.0,7384473.0,E MTAB 13196:Etv2Kaede WT S7 L001,0:28 1:98,A:258539610;C:211017108;G:209074684;T:251641766;N:170430,28,98,,,258539610,211017108,209074684,251641766,170430,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00355,0.88938,0.00148,0.14297,0.99569,0.83358,0.35626,0.53314,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11769,ERR11758631,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz,fastq fastq,1947733326.0,15458201.0,E MTAB 13196:Etv2 Traver S10 L001,0:28 1:98,A:532150077;C:434208725;G:472140578;T:508906834;N:327112,28,98,,,532150077,434208725,472140578,508906834,327112,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00677,0.92596,0.00142,0.07895,0.98526,0.85123,0.42802,0.53518,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11770,ERR11758646,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz,fastq fastq,1091426920.0,8801830.0,E MTAB 13196:Etv2 Traver S28 L001,0:26 1:98,A:302665480;C:247712584;G:269795015;T:271081940;N:171901,26,98,,,302665480,247712584,269795015,271081940,171901,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00585,0.90012,0.00149,0.07225,0.98746,0.84916,0.39007,0.54873,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11771,ERR11758602,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz,fastq fastq,983616732.0,7932393.0,E MTAB 13196:Etv2 Traver S25 L001,0:26 1:98,A:272974243;C:222949925;G:242884450;T:244652916;N:155198,26,98,,,272974243,222949925,242884450,244652916,155198,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00571,0.90139,0.00143,0.07484,0.98756,0.85019,0.40119,0.54977,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11772,ERR11758647,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz,fastq fastq,1162223232.0,9372768.0,E MTAB 13196:Etv2 Traver S27 L001,0:26 1:98,A:322910431;C:262934167;G:286614718;T:289578468;N:185448,26,98,,,322910431,262934167,286614718,289578468,185448,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00563,0.89924,0.00128,0.07464,0.98762,0.85064,0.38525,0.53889,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11773,ERR11758634,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz,fastq fastq,1979462268.0,15710018.0,E MTAB 13196:Etv2 Traver S12 L001,0:28 1:98,A:539088187;C:442520328;G:480420115;T:517077908;N:355730,28,98,,,539088187,442520328,480420115,517077908,355730,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00707,0.9236,0.00137,0.07727,0.98451,0.85021,0.41845,0.56136,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11774,ERR11758642,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz,fastq fastq,1809560214.0,14361589.0,E MTAB 13196:Etv2 Traver S9 L001,0:28 1:98,A:493206820;C:403886293;G:438502430;T:473641472;N:323199,28,98,,,493206820,403886293,438502430,473641472,323199,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00668,0.92354,0.00141,0.0785,0.98543,0.84938,0.43326,0.52002,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11775,ERR11758623,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz,fastq fastq,1074533780.0,8665595.0,E MTAB 13196:Etv2 Traver S26 L001,0:26 1:98,A:298569273;C:243430874;G:265536499;T:266825982;N:171152,26,98,,,298569273,243430874,265536499,266825982,171152,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00579,0.90109,0.00136,0.07564,0.98788,0.85017,0.3554,0.54362,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11776,ERR11758596,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz,fastq fastq,2167279758.0,17200633.0,E MTAB 13196:Etv2 Traver S11 L001,0:28 1:98,A:591928396;C:482735357;G:524267488;T:567952272;N:396245,28,98,,,591928396,482735357,524267488,567952272,396245,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00635,0.92351,0.00136,0.07835,0.9865,0.85204,0.41521,0.53672,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11777,ERR11758595,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz,fastq fastq,211593816.0,1679316.0,E MTAB 13196:drl h2b dendra tb S36 L001,0:28 1:98,A:62689430;C:45809168;G:45709128;T:57272091;N:113999,28,98,,,62689430,45809168,45709128,57272091,113999,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00192,0.91331,0.00072,0.14588,0.99675,0.89292,0.51304,0.63144,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11778,ERR11758629,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz,fastq fastq,980164836.0,7779086.0,E MTAB 13196:drl h2b dendra tb S37 L001,0:28 1:98,A:281375011;C:216067640;G:222839674;T:259781180;N:101331,28,98,,,281375011,216067640,222839674,259781180,101331,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00817,0.89718,0.00237,0.12153,0.98912,0.82643,0.46403,0.64954,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11779,ERR11758618,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz,fastq fastq,12118302.0,96177.0,E MTAB 13196:drl h2b dendra tb S39 L001,0:28 1:98,A:3543790;C:2662872;G:2728134;T:3182383;N:1123,28,98,,,3543790,2662872,2728134,3182383,1123,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00786,0.88963,0.0025,0.12543,0.99403,0.88635,0.50098,0.64694,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11780,ERR11758643,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz,fastq fastq,2061022698.0,16357323.0,E MTAB 13196:drl h2b dendra tb S5 L005,0:28 1:98,A:587730953;C:457631700;G:470283474;T:545196979;N:179592,28,98,,,587730953,457631700,470283474,545196979,179592,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01192,0.91661,0.00336,0.12397,0.98518,0.82568,0.45692,0.65555,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11781,ERR11758610,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz,fastq fastq,924603120.0,7338120.0,E MTAB 13196:drl h2b dendra tb S38 L001,0:28 1:98,A:265987815;C:203824483;G:210024160;T:244670646;N:96016,28,98,,,265987815,203824483,210024160,244670646,96016,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00773,0.89881,0.00242,0.12145,0.98944,0.82948,0.50529,0.66568,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11782,ERR11758641,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz,fastq fastq,1954661562.0,15513187.0,E MTAB 13196:drl h2b dendra tb S6 L005,0:28 1:98,A:558769608;C:433724557;G:445550100;T:516443984;N:173313,28,98,,,558769608,433724557,445550100,516443984,173313,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0125,0.91697,0.00373,0.12359,0.98447,0.82558,0.4881,0.6456,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11783,ERR11758591,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz,fastq fastq,4717188.0,37438.0,E MTAB 13196:drl h2b dendra tb S35 L001,0:28 1:98,A:1419430;C:1014265;G:1016661;T:1264642;N:2190,28,98,,,1419430,1014265,1016661,1264642,2190,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0012,0.65482,0.00054,0.10783,0.99953,0.97157,0.625,0.63689,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11784,ERR11758606,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz,fastq fastq,303645636.0,2409886.0,E MTAB 13196:drl h2b dendra tb S34 L001,0:28 1:98,A:90748559;C:65369482;G:65969002;T:81405258;N:153335,28,98,,,90748559,65369482,65969002,81405258,153335,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00228,0.91262,0.00099,0.14666,0.99638,0.89006,0.47177,0.63109,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11785,ERR11758640,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz,fastq fastq,661361022.0,5248897.0,E MTAB 13196:drl h2b dendra tb S40 L001,0:28 1:98,A:190087869;C:145985661;G:150124621;T:175095762;N:67109,28,98,,,190087869,145985661,150124621,175095762,67109,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00785,0.89784,0.00251,0.12159,0.98948,0.83055,0.46095,0.64951,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11786,ERR11758605,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz,fastq fastq,25157790.0,199665.0,E MTAB 13196:drl h2b dendra tb S7 L005,0:28 1:98,A:7330053;C:5600451;G:5635840;T:6589498;N:1948,28,98,,,7330053,5600451,5635840,6589498,1948,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01201,0.91385,0.00341,0.12826,0.98595,0.85161,0.49226,0.64953,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11787,ERR11758600,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz,fastq fastq,1422735804.0,11291554.0,E MTAB 13196:drl h2b dendra tb S8 L005,0:28 1:98,A:405788442;C:317299433;G:322206476;T:377317416;N:124037,28,98,,,405788442,317299433,322206476,377317416,124037,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01226,0.91547,0.0037,0.12565,0.9849,0.83662,0.48279,0.64531,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11788,ERR11758616,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz,fastq fastq,328918212.0,2610462.0,E MTAB 13196:drl h2b dendra tb S33 L001,0:28 1:98,A:98036464;C:71090137;G:71650807;T:87969481;N:171323,28,98,,,98036464,71090137,71650807,87969481,171323,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00197,0.89969,0.00087,0.14269,0.99681,0.89134,0.49763,0.63651,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11789,ERR11758588,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S12_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S12_L005_R1_001.fastq.gz,fastq fastq,970032168.0,7698668.0,E MTAB 13196:drl h2b dendra 22hpf S12 L005,0:28 1:98,A:268176072;C:223973927;G:223251001;T:254545365;N:85803,28,98,,,268176072,223973927,223251001,254545365,85803,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00525,0.91336,0.00127,0.06812,0.98995,0.85395,0.40891,0.4918,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11790,ERR11758597,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S42_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S42_L001_R1_001.fastq.gz,fastq fastq,716572206.0,5687081.0,E MTAB 13196:drl h2b dendra 22hpf S42 L001,0:28 1:98,A:198614388;C:164584363;G:164633280;T:188663484;N:76691,28,98,,,198614388,164584363,164633280,188663484,76691,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00366,0.8889,0.00092,0.06467,0.99261,0.84946,0.41353,0.49235,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11791,ERR11758637,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S44_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S44_L001_R1_001.fastq.gz,fastq fastq,481216932.0,3819182.0,E MTAB 13196:drl h2b dendra 22hpf S44 L001,0:28 1:98,A:133704525;C:110630722;G:110586099;T:126246571;N:49015,28,98,,,133704525,110630722,110586099,126246571,49015,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00352,0.89199,0.00099,0.06481,0.99308,0.85251,0.50101,0.49137,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11792,ERR11758617,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S41_L001_R1_001.fastq.gz drl_h2b-dendra_22hpf_S41_L001_R2_001.fastq.gz,fastq fastq,690504570.0,5480195.0,E MTAB 13196:drl h2b dendra 22hpf S41 L001,0:28 1:98,A:191676994;C:159013582;G:158945690;T:180795403;N:72901,28,98,,,191676994,159013582,158945690,180795403,72901,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00342,0.89103,0.00091,0.06637,0.99289,0.85196,0.42362,0.49417,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11793,ERR11758627,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S10_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S10_L005_R1_001.fastq.gz,fastq fastq,1443584898.0,11457023.0,E MTAB 13196:drl h2b dendra 22hpf S10 L005,0:28 1:98,A:398056083;C:333283767;G:332935857;T:379178009;N:131182,28,98,,,398056083,333283767,332935857,379178009,131182,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00494,0.91295,0.00128,0.06617,0.99101,0.84855,0.40479,0.49207,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11794,ERR11758609,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S40_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S40_L001_R1_001.fastq.gz,fastq fastq,139186908.0,1104658.0,E MTAB 13196:drl h2b dendra 22hpf S40 L001,0:28 1:98,A:39986504;C:31169749;G:30838192;T:37121531;N:70932,28,98,,,39986504,31169749,30838192,37121531,70932,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00113,0.88601,0.00057,0.08145,0.99801,0.89808,0.48148,0.48722,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11795,ERR11758633,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S39_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S39_L001_R1_001.fastq.gz,fastq fastq,226310742.0,1796117.0,E MTAB 13196:drl h2b dendra 22hpf S39 L001,0:28 1:98,A:64619137;C:51094203;G:50285631;T:60191319;N:120452,28,98,,,64619137,51094203,50285631,60191319,120452,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00116,0.89046,0.00054,0.07999,0.99797,0.89739,0.58119,0.48393,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11796,ERR11758604,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S9_L005_R1_001.fastq.gz drl_h2b-dendra_22hpf_S9_L005_R2_001.fastq.gz,fastq fastq,1419705504.0,11267504.0,E MTAB 13196:drl h2b dendra 22hpf S9 L005,0:28 1:98,A:390831393;C:328833478;G:328344998;T:371567158;N:128477,28,98,,,390831393,328833478,328344998,371567158,128477,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00519,0.91357,0.00132,0.0668,0.99042,0.84883,0.46254,0.47002,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11797,ERR11758608,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S43_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S43_L001_R1_001.fastq.gz,fastq fastq,744179814.0,5906189.0,E MTAB 13196:drl h2b dendra 22hpf S43 L001,0:28 1:98,A:206745595;C:171274047;G:171089532;T:194990120;N:80520,28,98,,,206745595,171274047,171089532,194990120,80520,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0033,0.89238,0.00092,0.06573,0.99348,0.85307,0.42184,0.45487,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11798,ERR11758625,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S11_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S11_L005_R1_001.fastq.gz,fastq fastq,1552027554.0,12317679.0,E MTAB 13196:drl h2b dendra 22hpf S11 L005,0:28 1:98,A:428241149;C:359820303;G:356746163;T:407080418;N:139521,28,98,,,428241149,359820303,356746163,407080418,139521,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00528,0.91344,0.00122,0.06856,0.98946,0.85667,0.46289,0.49059,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11799,ERR11758594,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S37_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S37_L001_R1_001.fastq.gz,fastq fastq,193604292.0,1536542.0,E MTAB 13196:drl h2b dendra 22hpf S37 L001,0:28 1:98,A:55140258;C:43966158;G:43414595;T:50989845;N:93436,28,98,,,55140258,43966158,43414595,50989845,93436,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00128,0.89527,0.00063,0.07949,0.99774,0.89538,0.424,0.48666,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11800,ERR11758639,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S38_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S38_L001_R1_001.fastq.gz,fastq fastq,226896894.0,1800769.0,E MTAB 13196:drl h2b dendra 22hpf S38 L001,0:28 1:98,A:65107594;C:50761930;G:50291626;T:60619991;N:115753,28,98,,,65107594,50761930,50291626,60619991,115753,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00111,0.88883,0.00057,0.07885,0.99807,0.89412,0.53921,0.47439,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11801,ERR11758636,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S31_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S31_L001_R2_001.fastq.gz,fastq fastq,188521452.0,1496202.0,E MTAB 13196:drl h2b dendra 12somites S31 L001,0:28 1:98,A:54946745;C:39757518;G:41515822;T:52209939;N:91428,28,98,,,54946745,39757518,41515822,52209939,91428,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00175,0.90844,0.00064,0.15428,0.99636,0.86393,0.39351,0.52017,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11802,ERR11758612,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S35_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S35_L001_R1_001.fastq.gz,fastq fastq,671596632.0,5330132.0,E MTAB 13196:drl h2b dendra 12somites S35 L001,0:28 1:98,A:189747551;C:145545792;G:153208485;T:183026617;N:68187,28,98,,,189747551,145545792,153208485,183026617,68187,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00594,0.90285,0.00156,0.12933,0.98823,0.80955,0.40956,0.53154,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11803,ERR11758620,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S36_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S36_L001_R1_001.fastq.gz,fastq fastq,456194592.0,3620592.0,E MTAB 13196:drl h2b dendra 12somites S36 L001,0:28 1:98,A:129689128;C:98798602;G:103687645;T:123970211;N:49006,28,98,,,129689128,98798602,103687645,123970211,49006,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00578,0.90274,0.00162,0.13523,0.98859,0.81917,0.43296,0.52776,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11804,ERR11758607,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S1_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S1_L005_R1_001.fastq.gz,fastq fastq,1313559828.0,10425078.0,E MTAB 13196:drl h2b dendra 12somites S1 L005,0:28 1:98,A:369071579;C:285484861;G:298845646;T:360037984;N:119758,28,98,,,369071579,285484861,298845646,360037984,119758,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00866,0.92327,0.00213,0.13248,0.98374,0.80846,0.41836,0.52646,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11805,ERR11758621,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S3_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S3_L005_R1_001.fastq.gz,fastq fastq,1400830452.0,11117702.0,E MTAB 13196:drl h2b dendra 12somites S3 L005,0:28 1:98,A:392932148;C:304653102;G:320171450;T:382949722;N:124030,28,98,,,392932148,304653102,320171450,382949722,124030,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0091,0.92525,0.00221,0.13204,0.98328,0.80683,0.39896,0.52474,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11806,ERR11758615,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S32_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S32_L001_R1_001.fastq.gz,fastq fastq,130164930.0,1033055.0,E MTAB 13196:drl h2b dendra 12somites S32 L001,0:28 1:98,A:38325421;C:27354135;G:28209607;T:36209402;N:66365,28,98,,,38325421,27354135,28209607,36209402,66365,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00164,0.90364,0.00061,0.16156,0.99651,0.87846,0.37878,0.51845,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11807,ERR11758590,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S34_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S34_L001_R1_001.fastq.gz,fastq fastq,806214402.0,6398527.0,E MTAB 13196:drl h2b dendra 12somites S34 L001,0:28 1:98,A:227716399;C:174839165;G:184278464;T:219297626;N:82748,28,98,,,227716399,174839165,184278464,219297626,82748,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00622,0.9021,0.00153,0.13047,0.98772,0.80866,0.40065,0.53454,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11808,ERR11758624,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S33_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S33_L001_R1_001.fastq.gz,fastq fastq,633634974.0,5028849.0,E MTAB 13196:drl h2b dendra 12somites S33 L001,0:28 1:98,A:179249875;C:137201579;G:144307176;T:172806546;N:69798,28,98,,,179249875,137201579,144307176,172806546,69798,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00585,0.90174,0.00155,0.12966,0.98831,0.80888,0.45862,0.52706,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11809,ERR11758626,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S4_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S4_L005_R1_001.fastq.gz,fastq fastq,927876096.0,7364096.0,E MTAB 13196:drl h2b dendra 12somites S4 L005,0:28 1:98,A:261732233;C:201837729;G:210685660;T:253535088;N:85386,28,98,,,261732233,201837729,210685660,253535088,85386,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00851,0.92329,0.00197,0.13519,0.98378,0.81665,0.41822,0.52852,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11810,ERR11758632,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S29_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S29_L001_R2_001.fastq.gz,fastq fastq,213074064.0,1691064.0,E MTAB 13196:drl h2b dendra 12somites S29 L001,0:28 1:98,A:62826305;C:44807633;G:46218609;T:59105445;N:116072,28,98,,,62826305,44807633,46218609,59105445,116072,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00163,0.90265,0.00072,0.1535,0.99701,0.87241,0.47674,0.51858,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11811,ERR11758592,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S2_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S2_L005_R1_001.fastq.gz,fastq fastq,1647474570.0,13075195.0,E MTAB 13196:drl h2b dendra 12somites S2 L005,0:28 1:98,A:462072903;C:358669639;G:376971859;T:449610611;N:149558,28,98,,,462072903,358669639,376971859,449610611,149558,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0086,0.92221,0.00193,0.12995,0.98285,0.80275,0.43249,0.52848,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11812,ERR11758611,ERX11157716,ERS16172934,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 12s,SAMEA114192241,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192241|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 12s|age:15|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:12 somite stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 12s|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 12s p,drl 12s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_12somites_S30_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S30_L001_R2_001.fastq.gz,fastq fastq,223279938.0,1772063.0,E MTAB 13196:drl h2b dendra 12somites S30 L001,0:28 1:98,A:64875575;C:47356253;G:49541812;T:61396530;N:109768,28,98,,,64875575,47356253,49541812,61396530,109768,ERX11157716,ERS16172934,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00168,0.90617,0.00068,0.15194,0.99669,0.86052,0.46907,0.52824,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26493,SRR26044865,SRX21761777,SRS18868295,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Rtf1MO single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX MO,GEX MO,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,MO-3GEX_S2_L002_R2_001.fastq.gz MO-3GEX_S2_L002_R1_001.fastq.gz MO-3GEX_S2_L002_I2_001.fastq.gz MO-3GEX_S2_L002_I1_001.fastq.gz MO-3GEX_S2_L001_R2_001.fastq.gz MO-3GEX_S2_L001_R1_001.fastq.gz MO-3GEX_S2_L001_I2_001.fastq.gz MO-3GEX_S2_L001_I1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,50770012872.0,367898644.0,MO 3GEX S2 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:10123747774;C:6493264924;G:7104700568;T:9387645989;N:1518705,10,10,28,90,10123747774,6493264924,7104700568,9387645989,1518705,SRX21761777,SRS18868295,SRA1710715,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.87322,,0.43479,,0.76881,,0.57534,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26494,SRR26044866,SRX21761776,SRS18868294,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Control single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX WT,GEX WT,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,WT-3GEX_S1_L001_I1_001.fastq.gz WT-3GEX_S1_L001_I2_001.fastq.gz WT-3GEX_S1_L001_R1_001.fastq.gz WT-3GEX_S1_L001_R2_001.fastq.gz WT-3GEX_S1_L002_I1_001.fastq.gz WT-3GEX_S1_L002_I2_001.fastq.gz WT-3GEX_S1_L002_R1_001.fastq.gz WT-3GEX_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,54878873586.0,397672997.0,WT 3GEX S1 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:10837179080;C:7155333415;G:7765967855;T:10030437304;N:1652076,10,10,28,90,10837179080,7155333415,7765967855,10030437304,1652076,SRX21761776,SRS18868294,SRA1710715,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.89445,,0.37406,,0.75481,,0.57841,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26495,SRR26044766,SRX21761676,SRS18868295,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Rtf1MO single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX MO,GEX MO,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,MO_3GEX_S2_L004_R2_001.fastq.gz MO_3GEX_S2_L004_R1_001.fastq.gz MO_3GEX_S2_L004_I2_001.fastq.gz MO_3GEX_S2_L004_I1_001.fastq.gz MO_3GEX_S2_L003_R2_001.fastq.gz MO_3GEX_S2_L003_R1_001.fastq.gz MO_3GEX_S2_L003_I2_001.fastq.gz MO_3GEX_S2_L003_I1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,2914080840.0,13245822.0,MO 3GEX S2 L003 I1 001.fastq.gz,0:10 1:10 2:100 3:100,A:726829083;C:402485666;G:452882760;T:1066890018;N:76873,10,10,100,100,726829083,402485666,452882760,1066890018,76873,SRX21761676,SRS18868295,SRA1710703,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",2,0.22802,0.87048,0.10701,0.42845,0.95595,0.77015,0.60757,0.57362,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26496,SRR26044767,SRX21761675,SRS18868294,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Control single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX WT,GEX WT,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,WT_3GEX_S1_L004_R2_001.fastq.gz WT_3GEX_S1_L004_R1_001.fastq.gz WT_3GEX_S1_L004_I2_001.fastq.gz WT_3GEX_S1_L004_I1_001.fastq.gz WT_3GEX_S1_L003_R2_001.fastq.gz WT_3GEX_S1_L003_R1_001.fastq.gz WT_3GEX_S1_L003_I2_001.fastq.gz WT_3GEX_S1_L003_I1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,4986906540.0,22667757.0,WT 3GEX S1 L003 I1 001.fastq.gz,0:10 1:10 2:100 3:100,A:1227427708;C:695004251;G:785531191;T:1825414315;N:173935,10,10,100,100,1227427708,695004251,785531191,1825414315,173935,SRX21761675,SRS18868294,SRA1710703,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",2,0.21872,0.89321,0.09696,0.36976,0.9558,0.75639,0.62213,0.46544,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26497,SRR26044613,SRX21761588,SRS18868295,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Rtf1MO single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX MO,GEX MO,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,MO_3GEX_S2_L002_R2_001.fastq.gz MO_3GEX_S2_L002_R1_001.fastq.gz MO_3GEX_S2_L002_I2_001.fastq.gz MO_3GEX_S2_L002_I1_001.fastq.gz MO_3GEX_S2_L001_R2_001.fastq.gz MO_3GEX_S2_L001_R1_001.fastq.gz MO_3GEX_S2_L001_I2_001.fastq.gz MO_3GEX_S2_L001_I1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,21527638854.0,155997383.0,MO 3GEX S2 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:4285470476;C:2755587559;G:3034249420;T:3964137056;N:319959,10,10,28,90,4285470476,2755587559,3034249420,3964137056,319959,SRX21761588,SRS18868295,SRA1710658,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.87277,,0.43202,,0.7725,,0.56861,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26498,SRR26044614,SRX21761587,SRS18868294,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,Control single cell Multiome GEX 11 12 somite stage,,strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal,,,,,,,,,10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq,GEX WT,GEX WT,Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459729,,,WT_3GEX_S1_L001_I1_001.fastq.gz WT_3GEX_S1_L001_I2_001.fastq.gz WT_3GEX_S1_L001_R1_001.fastq.gz WT_3GEX_S1_L001_R2_001.fastq.gz WT_3GEX_S1_L002_I1_001.fastq.gz WT_3GEX_S1_L002_I2_001.fastq.gz WT_3GEX_S1_L002_R1_001.fastq.gz WT_3GEX_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,24359922978.0,176521181.0,WT 3GEX S1 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:4802729436;C:3179460152;G:3468651943;T:4435697892;N:366867,10,10,28,90,4802729436,3179460152,3468651943,4435697892,366867,SRX21761587,SRS18868294,SRA1710658,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.89475,,0.37342,,0.75668,,0.45872,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2023-09-12,Segmentation,Embryo,Whole Organism,All anatomical structures
26536,SRR26130973,SRX21844394,SRS18942411,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X49 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 6|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo6,10X49 2,10X49 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X49_2_S5_L001_R1_001.fastq.gz 10X49_2_S5_L001_R2_001.fastq.gz 10X49_2_S5_L002_R1_001.fastq.gz 10X49_2_S5_L002_R2_001.fastq.gz 10X49_2_S5_L003_R1_001.fastq.gz 10X49_2_S5_L003_R2_001.fastq.gz 10X49_2_S5_L004_R1_001.fastq.gz 10X49_2_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3126113844.0,37215641.0,10X49 2 S5 L001 R1 001.fastq.gz,0:28 1:56,A:898881980;C:657306128;G:664563758;T:905262774;N:99204,28,56,,,898881980,657306128,664563758,905262774,99204,SRX21844394,SRS18942411,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01241,0.88203,0.00542,0.35268,0.98129,0.7586,0.40274,0.5074,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26537,SRR26130974,SRX21844393,SRS18942407,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X49 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 5|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo5,10X49 1,10X49 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X49_1_S4_L001_R1_001.fastq.gz 10X49_1_S4_L001_R2_001.fastq.gz 10X49_1_S4_L002_R1_001.fastq.gz 10X49_1_S4_L002_R2_001.fastq.gz 10X49_1_S4_L003_R1_001.fastq.gz 10X49_1_S4_L003_R2_001.fastq.gz 10X49_1_S4_L004_R1_001.fastq.gz 10X49_1_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3315364752.0,39468628.0,10X49 1 S4 L001 R1 001.fastq.gz,0:28 1:56,A:957164498;C:690985782;G:704099796;T:963009918;N:104758,28,56,,,957164498,690985782,704099796,963009918,104758,SRX21844393,SRS18942407,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.0143,0.88325,0.00601,0.35854,0.97816,0.75868,0.4158,0.50825,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26538,SRR26130975,SRX21844392,SRS18942399,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X47 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 4|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo4,10X47 2,10X47 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X47_2_S2_L001_R1_001.fastq.gz 10X47_2_S2_L001_R2_001.fastq.gz 10X47_2_S2_L002_R1_001.fastq.gz 10X47_2_S2_L002_R2_001.fastq.gz 10X47_2_S2_L003_R1_001.fastq.gz 10X47_2_S2_L003_R2_001.fastq.gz 10X47_2_S2_L004_R1_001.fastq.gz 10X47_2_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3525979800.0,41975950.0,10X47 2 S2 L001 R1 001.fastq.gz,0:28 1:56,A:1030048762;C:725438274;G:855378888;T:915005070;N:108806,28,56,,,1030048762,725438274,855378888,915005070,108806,SRX21844392,SRS18942399,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.0126,0.69252,0.00546,0.25721,0.98005,0.85295,0.39068,0.51992,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26539,SRR26130976,SRX21844391,SRS18942406,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X47 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 3|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo3,10X47 1,10X47 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X47_1_S1_L001_R1_001.fastq.gz 10X47_1_S1_L001_R2_001.fastq.gz 10X47_1_S1_L002_R1_001.fastq.gz 10X47_1_S1_L002_R2_001.fastq.gz 10X47_1_S1_L003_R1_001.fastq.gz 10X47_1_S1_L003_R2_001.fastq.gz 10X47_1_S1_L004_R1_001.fastq.gz 10X47_1_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3288490212.0,39148693.0,10X47 1 S1 L001 R1 001.fastq.gz,0:28 1:56,A:950740376;C:692224998;G:723085676;T:922337432;N:101730,28,56,,,950740376,692224998,723085676,922337432,101730,SRX21844391,SRS18942406,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01086,0.86383,0.0052,0.31674,0.98244,0.78309,0.39399,0.52299,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26540,SRR26130977,SRX21844390,SRS18942410,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X39 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 2|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo2,10X39 2,10X39 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X39_2_S2_L001_R1_001.fastq.gz 10X39_2_S2_L001_R2_001.fastq.gz 10X39_2_S2_L002_R1_001.fastq.gz 10X39_2_S2_L002_R2_001.fastq.gz 10X39_2_S2_L003_R1_001.fastq.gz 10X39_2_S2_L003_R2_001.fastq.gz 10X39_2_S2_L004_R1_001.fastq.gz 10X39_2_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,20594785932.0,245176023.0,10X39 2 S2 L001 R1 001.fastq.gz,0:28 1:56,A:5909286071;C:4378110318;G:4489721587;T:5804002561;N:13665395,28,56,,,5909286071,4378110318,4489721587,5804002561,13665395,SRX21844390,SRS18942410,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01117,0.90005,0.00416,0.25843,0.98056,0.77926,0.45338,0.53366,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26541,SRR26130978,SRX21844389,SRS18942405,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X39 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 1|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo1,10X39 1,10X39 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X39_1_S1_L004_R2_001.fastq.gz 10X39_1_S1_L004_R1_001.fastq.gz 10X39_1_S1_L003_R2_001.fastq.gz 10X39_1_S1_L003_R1_001.fastq.gz 10X39_1_S1_L002_R2_001.fastq.gz 10X39_1_S1_L002_R1_001.fastq.gz 10X39_1_S1_L001_R2_001.fastq.gz 10X39_1_S1_L001_R1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,13293718116.0,158258549.0,10X39 1 S1 L001 R1 001.fastq.gz,0:28 1:56,A:3791388201;C:2833705086;G:2863082386;T:3796683434;N:8859009,28,56,,,3791388201,2833705086,2863082386,3796683434,8859009,SRX21844389,SRS18942405,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01078,0.90504,0.00392,0.24179,0.98098,0.77741,0.42922,0.52858,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
31963,SRR28832522,SRX24395271,SRS21150709,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,7b,,strain:ABC|dev stage:7 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,7b,7b,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,7b_concatenated_R1.fastq.gz 7b_concatenated_R2.fastq.gz,fastq fastq,67688938179.0,524720451.0,7b concatenated R1.fastq.gz,0:28 1:101,A:18993507272;C:15386021146;G:15634918803;T:17652028346;N:22462612,28,101,,,18993507272,15386021146,15634918803,17652028346,22462612,SRX24395271,SRS21150709,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31964,SRR28832523,SRX24395270,SRS21150708,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,7a,,strain:ABC|dev stage:7 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,7a,7a,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,7a_concatenated_R1.fastq.gz 7a_concatenated_R2.fastq.gz,fastq fastq,79101784254.0,613192126.0,7a concatenated R1.fastq.gz,0:28 1:101,A:22179167002;C:18012103520;G:18280647088;T:20603509593;N:26357051,28,101,,,22179167002,18012103520,18280647088,20603509593,26357051,SRX24395270,SRS21150708,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31965,SRR28832524,SRX24395269,SRS21150710,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,6b,,strain:ABC|dev stage:6 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,6b,6b,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,6b_concatenated_R1.fastq.gz 6b_concatenated_R2.fastq.gz,fastq fastq,69567742683.0,539284827.0,6b concatenated R1.fastq.gz,0:28 1:101,A:19762887143;C:15877063714;G:15450633995;T:18460750107;N:16407724,28,101,,,19762887143,15877063714,15450633995,18460750107,16407724,SRX24395269,SRS21150710,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31966,SRR28832525,SRX24395268,SRS21150711,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,6a,,strain:ABC|dev stage:6 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,6a,6a,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,6a_concatenated_R1.fastq.gz 6a_concatenated_R2.fastq.gz,fastq fastq,69092868528.0,535603632.0,6a concatenated R1.fastq.gz,,,,,,,,,,,,SRX24395268,SRS21150711,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31967,SRR28832526,SRX24395267,SRS21150707,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,5c,,strain:ABC|dev stage:5 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate C|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,5c,5c,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,5c_concatenated_R1.fastq.gz 5c_concatenated_R2.fastq.gz,fastq fastq,42738149952.0,331303488.0,5c concatenated R1.fastq.gz,0:28 1:101,A:12472930469;C:9646780605;G:9513754487;T:11098062350;N:6622041,28,101,,,12472930469,9646780605,9513754487,11098062350,6622041,SRX24395267,SRS21150707,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31968,SRR28832527,SRX24395266,SRS21150706,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,4b,,strain:ABC|dev stage:4 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,4b,4b,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,4b_concatenated_R1.fastq.gz 4b_concatenated_R2.fastq.gz,fastq fastq,71168549994.0,551694186.0,4b concatenated R1.fastq.gz,0:28 1:101,A:19966236558;C:16224236063;G:16033442126;T:18882486499;N:62148748,28,101,,,19966236558,16224236063,16033442126,18882486499,62148748,SRX24395266,SRS21150706,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31969,SRR28832528,SRX24395265,SRS21150705,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,4a,,strain:ABC|dev stage:4 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,4a,4a,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,4a_concatenated_R1.fastq.gz 4a_concatenated_R2.fastq.gz,fastq fastq,68732228646.0,532807974.0,4a concatenated R1.fastq.gz,0:28 1:101,A:19390338294;C:15653316754;G:15467157018;T:18205511068;N:15905512,28,101,,,19390338294,15653316754,15467157018,18205511068,15905512,SRX24395265,SRS21150705,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31970,SRR28832529,SRX24395264,SRS21150704,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,3b,,strain:ABC|dev stage:3 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,3b,3b,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,3b_concatenated_R1.fastq.gz 3b_concatenated_R2.fastq.gz,fastq fastq,64966771536.0,503618384.0,3b concatenated R1.fastq.gz,0:28 1:101,A:18187699043;C:14602482735;G:14672400468;T:17481975446;N:22213844,28,101,,,18187699043,14602482735,14672400468,17481975446,22213844,SRX24395264,SRS21150704,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
31971,SRR28832530,SRX24395263,SRS21150703,SRP504662,PRJNA1105232,Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens,PRJNA1105232,Other,The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.,,,,,3a,,strain:ABC|dev stage:3 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish larvae,3a,3a,10X Chromium,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP504662,,,3a_concatenated_R1.fastq.gz 3a_concatenated_R2.fastq.gz,fastq fastq,68966162664.0,534621416.0,3a concatenated R1.fastq.gz,0:28 1:101,A:19232364475;C:15520559864;G:15732756322;T:18456921265;N:23560738,28,101,,,19232364475,15520559864,15732756322,18456921265,23560738,SRX24395263,SRS21150703,SRA1854140,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2024-04-29,Larval,Larval,Whole Organism,All anatomical structures
60657,SRR15046102,SRX11356738,SRS9403587,SRP278034,PRJNA657343,Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development,PRJNA657343,Other,Comprehensive integration of transcriptome  genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.,,,scRNAseq,scRNAseq Satb2 MUT 14som,scRNAseq Satb2 MUT 14som,,strain:Satb2 Mutant|age:14 somite|dev stage:14 somite|sex:not applicable|tissue:whole embryo|replicate:replicate = Biological replicate1|BioSampleModel:Model organism or animal,,,,,,,,,Satb2 mutants single cell RNAseq,Satb2 MUT 14ss scRNAseq,Satb2 MUT 14ss scRNAseq,according 10X three primemRNA seq V3.2 protocol,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 550,,SRP278034,,loader:fastq load.py,,,23142978710.0,177123922.0,scRNAseq Satb2 MUT 14som I1.fastq.gz,0:8 1:30 2:92.66,A:4753575949;C:3375880000;G:3751151628;T:4500225651;N:31436446,8,30,92,,4753575949,3375880000,3751151628,4500225651,31436446,SRX11356738,SRS9403587,SRA1254741,IISER-PUNE|biology,IISER-PUNE,1,0.80351,,0.14479,,0.79695,,0.55274,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,India,2021-07-13,Segmentation,Embryo,Whole Organism,All anatomical structures
60658,SRR15046103,SRX11356737,SRS9403586,SRP278034,PRJNA657343,Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development,PRJNA657343,Other,Comprehensive integration of transcriptome  genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.,,,scRNAseq,scRNAseq WT 14som,scRNAseq WT 14som,,strain:Wild type sibling|age:14 somite|dev stage:14 somite|sex:not applicable|tissue:whole embryo|replicate:replicate = Biological replicate1|BioSampleModel:Model organism or animal,,,,,,,,,Satb2 siblings single cell RNAseq,WT sibs 14ss scRNAseq,WT sibs 14ss scRNAseq,according 10X three primemRNA seq V3.2 protocol,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 550,,SRP278034,,loader:fastq load.py|options:  mixedDeflines   maxErrorCount=0,,,27847103625.0,200338875.0,scRNAseq WT 14som I1.fastq.gz,0:8 1:30 2:101,A:5948912529;C:4138132473;G:4588280753;T:5527087357;N:31813263,8,30,101,,5948912529,4138132473,4588280753,5527087357,31813263,SRX11356737,SRS9403586,SRA1254741,IISER-PUNE|biology,IISER-PUNE,1,0.92298,,0.15133,,0.78906,,0.54933,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,India,2021-07-13,Segmentation,Embryo,Whole Organism,All anatomical structures
70700,SRR21457006,SRX17460727,SRS15014538,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Hepatized intestine in lbw S1 L002,,isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf lbw mutant intestine,LG S1 L002  aliquot 2,LG S1 L002  aliquot 2,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S1_LG_20200825NB_S1_L002_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L002_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L002_R2_001.fastq.gz,fastq fastq fastq,14193607989.0,75901647.0,20200806 S1 LG 20200825NB S1 L002 I1 001.fastq.gz,0:8 1:28 2:151,A:3301648645;C:2611036971;G:2734265669;T:2814086798;N:110614,8,28,151,,3301648645,2611036971,2734265669,2814086798,110614,SRX17460727,SRS15014538,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.91108,,0.11686,,0.85557,,0.57466,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70701,SRR21457007,SRX17460726,SRS15014537,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Hepatized intestine in lbw S1 L001,,isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 1|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf lbw mutant intestine,LG S1 L001  aliquot 1,LG S1 L001  aliquot 1,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S1_LG_20200825NB_S1_L001_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L001_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L001_R2_001.fastq.gz,fastq fastq fastq,14182591632.0,75842736.0,20200806 S1 LG 20200825NB S1 L001 I1 001.fastq.gz,0:8 1:28 2:151,A:3299405296;C:2608368813;G:2735448901;T:2808939262;N:90864,8,28,151,,3299405296,2608368813,2735448901,2808939262,90864,SRX17460726,SRS15014537,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.91027,,0.11587,,0.85587,,0.72332,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70702,SRR21457008,SRX17460725,SRS15014536,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Intestine in the WT S2 L004,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 4|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type intestine,Gut S2 L004  aliquot 4,Gut S2 L004  aliquot 4,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S2_Gut_20200825NB_S2_L004_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L004_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L004_R2_001.fastq.gz,fastq fastq fastq,16914022840.0,90449320.0,20200806 S2 Gut 20200825NB S2 L004 I1 001.fastq.gz,0:8 1:28 2:151,A:4133386049;C:3106166206;G:3057574159;T:3360630096;N:90810,8,28,151,,4133386049,3106166206,3057574159,3360630096,90810,SRX17460725,SRS15014536,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.92139,,0.0763,,0.88294,,0.43703,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70703,SRR21457009,SRX17460724,SRS15014535,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Intestine in the WT S2 L003,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 3|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type intestine,Gut S2 L003  aliquot 3,Gut S2 L003  aliquot 3,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S2_Gut_20200825NB_S2_L003_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L003_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L003_R2_001.fastq.gz,fastq fastq fastq,16982190885.0,90813855.0,20200806 S2 Gut 20200825NB S2 L003 I1 001.fastq.gz,0:8 1:28 2:151,A:4147484891;C:3121909538;G:3068007254;T:3375339308;N:151114,8,28,151,,4147484891,3121909538,3068007254,3375339308,151114,SRX17460724,SRS15014535,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.92489,,0.07717,,0.88264,,0.74722,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70704,SRR21457010,SRX17460723,SRS15014534,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Intestine in the WT S2 L002,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type intestine,Gut S2 L002  aliquot 2,Gut S2 L002  aliquot 2,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S2_Gut_20200825NB_S2_L002_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L002_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L002_R2_001.fastq.gz,fastq fastq fastq,16821098800.0,89952400.0,20200806 S2 Gut 20200825NB S2 L002 I1 001.fastq.gz,0:8 1:28 2:151,A:4111764153;C:3090100433;G:3032700332;T:3348115120;N:132362,8,28,151,,4111764153,3090100433,3032700332,3348115120,132362,SRX17460723,SRS15014534,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.92867,,0.07772,,0.88162,,0.75163,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70705,SRR21457011,SRX17460722,SRS15014533,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Intestine in the WT S2 L001,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 1|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type intestine,Gut S2 L001  aliquot 1,Gut S2 L001  aliquot 1,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S2_Gut_20200825NB_S2_L001_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L001_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L001_R2_001.fastq.gz,fastq fastq fastq,16838878760.0,90047480.0,20200806 S2 Gut 20200825NB S2 L001 I1 001.fastq.gz,0:8 1:28 2:151,A:4115908576;C:3092172269;G:3039279605;T:3349698554;N:110476,8,28,151,,4115908576,3092172269,3039279605,3349698554,110476,SRX17460722,SRS15014533,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.92762,,0.07664,,0.88172,,0.73829,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70706,SRR21457012,SRX17460721,SRS15014532,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L004,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 4|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L004  aliquot 4,Live S4 L004  aliquot 4,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L004_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R2_001.fastq.gz,fastq fastq fastq,15359722785.0,82137555.0,20200806 S4 Live 20200825NB S4 L004 I1 001.fastq.gz,0:8 1:28 2:151,A:3860252969;C:2756020453;G:2781498176;T:3004915512;N:83695,8,28,151,,3860252969,2756020453,2781498176,3004915512,83695,SRX17460721,SRS15014532,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90519,,0.06757,,0.88243,,0.74961,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System
70707,SRR21457013,SRX17460720,SRS15014531,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L003,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 3|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L003  aliquot 3,Live S4 L003  aliquot 3,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L003_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R2_001.fastq.gz,fastq fastq fastq,15277905984.0,81700032.0,20200806 S4 Live 20200825NB S4 L003 I1 001.fastq.gz,0:8 1:28 2:151,A:3834498109;C:2745604041;G:2766967723;T:2989497144;N:137815,8,28,151,,3834498109,2745604041,2766967723,2989497144,137815,SRX17460720,SRS15014531,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90792,,0.06795,,0.88089,,0.75291,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System
70708,SRR21457014,SRX17460719,SRS15014530,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Hepatized intestine in lbw S1 L004,,isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 4|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf lbw mutant intestine,LG S1 L004  aliquot 4,LG S1 L004  aliquot 4,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S1_LG_20200825NB_S1_L004_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L004_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L004_R2_001.fastq.gz,fastq fastq fastq,14467696881.0,77367363.0,20200806 S1 LG 20200825NB S1 L004 I1 001.fastq.gz,0:8 1:28 2:151,A:3365177661;C:2661264013;G:2793822598;T:2862129575;N:77966,8,28,151,,3365177661,2661264013,2793822598,2862129575,77966,SRX17460719,SRS15014530,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90564,,0.11415,,0.85669,,0.72469,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70709,SRR21457015,SRX17460718,SRS15014529,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Hepatized intestine in lbw S1 L003,,isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 3|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf lbw mutant intestine,LG S1 L003  aliquot 3,LG S1 L003  aliquot 3,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S1_LG_20200825NB_S1_L003_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L003_R2_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L003_I1_001.fastq.gz,fastq fastq fastq,14438452138.0,77210974.0,20200806 S1 LG 20200825NB S1 L003 I1 001.fastq.gz,0:8 1:28 2:151,A:3354566334;C:2659200277;G:2787479629;T:2857478988;N:131846,8,28,151,,3354566334,2659200277,2787479629,2857478988,131846,SRX17460718,SRS15014529,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90915,,0.11415,,0.85427,,0.7235,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Gut,Digestive System
70710,SRR21457016,SRX17460717,SRS15014528,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine  we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L002,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L002  aliquot 2,Live S4 L002  aliquot 2,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L002_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R2_001.fastq.gz,fastq fastq fastq,15033903335.0,80395205.0,20200806 S4 Live 20200825NB S4 L002 I1 001.fastq.gz,0:8 1:28 2:151,A:3774023536;C:2701104584;G:2719224706;T:2945204367;N:118762,8,28,151,,3774023536,2701104584,2719224706,2945204367,118762,SRX17460717,SRS15014528,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90993,,0.06896,,0.88002,,0.75003,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System