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125 rows where experiment.library_selection = "Oligo-dT" and experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL"

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devstage_curation 6

devstage_curation_coarse 4

technology 3

experiment.library_layout 2

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 125 ✖

experiment.library_selection 1

  • Oligo-dT · 125 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
10163 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 t…         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 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 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 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 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 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 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 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 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 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 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 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 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 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

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