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357 rows where experiment.platform = "ILLUMINA", technology = "10x" and tissue_curation_coarse = "Multi-system"

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devstage_curation 6

experiment.library_selection 5

devstage_curation_coarse 4

tissue_curation 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Multi-system · 357 ✖

technology 1

  • 10x · 357 ✖

experiment.platform 1

  • ILLUMINA · 357 ✖
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
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
10403 10403 ERR8527374 ERX8137561 ERS10539829 ERP135430 PRJEB50826 scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E-MTAB-11079_2 Transcriptome Analysis Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10   Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. ZF2 SAMEA12941033 University Of Edinburgh ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK                 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E MTAB 11079 2:ZF2 p ZF2 p scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Experimental Factor: phenotype:ren knockout RNA-Seq TRANSCRIPTOMIC SINGLE CELL size fractionation PAIRED ILLUMINA NextSeq 500   ERP135430 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz fastq fastq fastq 38557081640.0 125185330.0 E MTAB 11079 2:ZF2 S2 L002 0:8 1:150 2:150 A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117 8 150 150   13781315856 6436030786 6578059630 10759631611 561117 ERX8137561 ERS10539829 ERA9016154 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.0 0.84449 0.0 0.09657 1.0 0.8242   0.52635 150 150 T B mate1 technical by mapping diff illumina nextseq unknown size_fractionation unknown sc single_cell_droplet 10x   United Kingdom 2022-06-10 Adult Adult Multi-tissue Multi-system
10404 10404 ERR8527377 ERX8137561 ERS10539829 ERP135430 PRJEB50826 scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E-MTAB-11079_2 Transcriptome Analysis Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10   Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. ZF2 SAMEA12941033 University Of Edinburgh ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK                 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E MTAB 11079 2:ZF2 p ZF2 p scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Experimental Factor: phenotype:ren knockout RNA-Seq TRANSCRIPTOMIC SINGLE CELL size fractionation PAIRED ILLUMINA NextSeq 500   ERP135430 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz fastq fastq fastq 38872269128.0 126208666.0 E MTAB 11079 2:ZF2 S2 L001 0:8 1:150 2:150 A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374 8 150 150   15151865400 6355030057 6591732598 9763441371 530374 ERX8137561 ERS10539829 ERA9016154 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.0 0.84526 0.0 0.09779 1.0 0.82609   0.54388 150 150 T B mate1 technical by mapping diff illumina nextseq unknown size_fractionation unknown sc single_cell_droplet 10x   United Kingdom 2022-06-10 Adult Adult Multi-tissue Multi-system
10405 10405 ERR8527376 ERX8137560 ERS10539828 ERP135430 PRJEB50826 scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E-MTAB-11079_2 Transcriptome Analysis Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10   Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. ZF1 SAMEA12941032 University Of Edinburgh ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK                 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E MTAB 11079 2:ZF1 p ZF1 p scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Experimental Factor: phenotype:wild type RNA-Seq TRANSCRIPTOMIC SINGLE CELL size fractionation PAIRED ILLUMINA NextSeq 500   ERP135430 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz fastq fastq fastq 39415722500.0 127973125.0 E MTAB 11079 2:ZF1 S1 L002 0:8 1:150 2:150 A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200 8 150 150   14261012964 6339158428 6467430919 11323758989 576200 ERX8137560 ERS10539828 ERA9016154 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.0 0.81065 0.0 0.08289 1.0 0.82434   0.52903 150 150 T B mate1 technical by mapping diff illumina nextseq unknown size_fractionation unknown sc single_cell_droplet 10x   United Kingdom 2022-06-10 Adult Adult Multi-tissue Multi-system
10406 10406 ERR8527375 ERX8137560 ERS10539828 ERP135430 PRJEB50826 scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E-MTAB-11079_2 Transcriptome Analysis Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10   Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. ZF1 SAMEA12941032 University Of Edinburgh ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK                 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish E MTAB 11079 2:ZF1 p ZF1 p scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Experimental Factor: phenotype:wild type RNA-Seq TRANSCRIPTOMIC SINGLE CELL size fractionation PAIRED ILLUMINA NextSeq 500   ERP135430 NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz fastq fastq fastq 39744721324.0 129041303.0 E MTAB 11079 2:ZF1 S1 L001 0:8 1:150 2:150 A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007 8 150 150   15670316830 6278039908 6505806971 10257683184 544007 ERX8137560 ERS10539828 ERA9016154 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 2 0.0 0.81031 0.0 0.08495 1.0 0.82169   0.51724 150 150 T B mate1 technical by mapping diff illumina nextseq unknown size_fractionation unknown sc single_cell_droplet 10x   United Kingdom 2022-06-10 Adult Adult Multi-tissue Multi-system
15614 15614 ERR13109732 ERX12481366 ERS19896183 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT young SAMEA115618603 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT young p WT young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_young_S16_L002_I1_001.fastq.gz WT_young_S16_L002_R1_001.fastq.gz WT_young_S16_L002_R2_001.fastq.gz fastq fastq fastq 11547230144.0 90923072.0 E MTAB 14075:WT young S16 L002 0:8 1:28 2:91 A:2298760158;C:1887715706;G:1977278606;T:2109839457;N:405625 8 28 91   2298760158 1887715706 1977278606 2109839457 405625 ERX12481366 ERS19896183 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15615 15615 ERR13109737 ERX12481366 ERS19896183 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT young SAMEA115618603 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT young p WT young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_young_run2_S10_L001_I1_001.fastq.gz WT_young_run2_S10_L001_R1_001.fastq.gz WT_young_run2_S10_L001_R2_001.fastq.gz fastq fastq fastq 6300899375.0 50407195.0 E MTAB 14075:WT young run2 S10 L001 0:8 1:28 2:89 A:1243074350;C:1030040216;G:1079454879;T:1133663108;N:7802 8 28 89   1243074350 1030040216 1079454879 1133663108 7802 ERX12481366 ERS19896183 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15616 15616 ERR13109733 ERX12481366 ERS19896183 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT young SAMEA115618603 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT young p WT young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_young_run2_S10_L002_I1_001.fastq.gz WT_young_run2_S10_L002_R1_001.fastq.gz WT_young_run2_S10_L002_R2_001.fastq.gz fastq fastq fastq 6323980500.0 50591844.0 E MTAB 14075:WT young run2 S10 L002 0:8 1:28 2:89 A:1248024810;C:1032976792;G:1082805513;T:1138855823;N:11178 8 28 89   1248024810 1032976792 1082805513 1138855823 11178 ERX12481366 ERS19896183 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15617 15617 ERR13109728 ERX12481366 ERS19896183 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT young SAMEA115618603 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT young p WT young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_young_S16_L001_I1_001.fastq.gz WT_young_S16_L001_R1_001.fastq.gz WT_young_S16_L001_R2_001.fastq.gz fastq fastq fastq 9395132467.0 73977421.0 E MTAB 14075:WT young S16 L001 0:8 1:28 2:91 A:1870197969;C:1535772308;G:1609450193;T:1716224344;N:300497 8 28 91   1870197969 1535772308 1609450193 1716224344 300497 ERX12481366 ERS19896183 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15618 15618 ERR13109727 ERX12481365 ERS19896182 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT aged SAMEA115618602 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT aged p WT aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_aged_S15_L001_I1_001.fastq.gz WT_aged_S15_L001_R1_001.fastq.gz WT_aged_S15_L001_R2_001.fastq.gz fastq fastq fastq 3224055528.0 25386264.0 E MTAB 14075:WT aged S15 L001 0:8 1:28 2:91 A:632762441;C:548488749;G:552881879;T:575917355;N:99600 8 28 91   632762441 548488749 552881879 575917355 99600 ERX12481365 ERS19896182 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15619 15619 ERR13109729 ERX12481365 ERS19896182 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT aged SAMEA115618602 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT aged p WT aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_aged_S15_L002_I1_001.fastq.gz WT_aged_S15_L002_R1_001.fastq.gz WT_aged_S15_L002_R2_001.fastq.gz fastq fastq fastq 4178136043.0 32898709.0 E MTAB 14075:WT aged S15 L002 0:8 1:28 2:91 A:820476445;C:710661272;G:715891121;T:746611018;N:142663 8 28 91   820476445 710661272 715891121 746611018 142663 ERX12481365 ERS19896182 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15620 15620 ERR13109731 ERX12481365 ERS19896182 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT aged SAMEA115618602 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT aged p WT aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_aged_run2_S13_L002_I1_001.fastq.gz WT_aged_run2_S13_L002_R1_001.fastq.gz WT_aged_run2_S13_L002_R2_001.fastq.gz fastq fastq fastq 11315635500.0 90525084.0 E MTAB 14075:WT aged run2 S13 L002 0:8 1:28 2:89 A:2205965370;C:1918372621;G:1938090305;T:1994285205;N:18975 8 28 89   2205965370 1918372621 1938090305 1994285205 18975 ERX12481365 ERS19896182 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15621 15621 ERR13109734 ERX12481365 ERS19896182 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. WT aged SAMEA115618602 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:WT aged p WT aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 WT_aged_run2_S13_L001_I1_001.fastq.gz WT_aged_run2_S13_L001_R1_001.fastq.gz WT_aged_run2_S13_L001_R2_001.fastq.gz fastq fastq fastq 11297009750.0 90376078.0 E MTAB 14075:WT aged run2 S13 L001 0:8 1:28 2:89 A:2201626807;C:1916371507;G:1936001373;T:1989457619;N:13636 8 28 89   2201626807 1916371507 1936001373 1989457619 13636 ERX12481365 ERS19896182 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15622 15622 ERR13109730 ERX12481363 ERS19896180 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het aged SAMEA115618600 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het aged p Het aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_aged_run2_S14_L002_I1_001.fastq.gz Het_aged_run2_S14_L002_R1_001.fastq.gz Het_aged_run2_S14_L002_R2_001.fastq.gz fastq fastq fastq 4755473375.0 38043787.0 E MTAB 14075:Het aged run2 S14 L002 0:8 1:28 2:89 A:924628155;C:804435427;G:826904786;T:829920091;N:8584 8 28 89   924628155 804435427 826904786 829920091 8584 ERX12481363 ERS19896180 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15623 15623 ERR13109738 ERX12481363 ERS19896180 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het aged SAMEA115618600 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het aged p Het aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_aged_run2_S14_L001_I1_001.fastq.gz Het_aged_run2_S14_L001_R1_001.fastq.gz Het_aged_run2_S14_L001_R2_001.fastq.gz fastq fastq fastq 4757077375.0 38056619.0 E MTAB 14075:Het aged run2 S14 L001 0:8 1:28 2:89 A:924804478;C:805146986;G:827570549;T:829511132;N:5946 8 28 89   924804478 805146986 827570549 829511132 5946 ERX12481363 ERS19896180 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15624 15624 ERR13109725 ERX12481363 ERS19896180 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het aged SAMEA115618600 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het aged p Het aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_aged_S13_L001_I1_001.fastq.gz Het_aged_S13_L001_R1_001.fastq.gz Het_aged_S13_L001_R2_001.fastq.gz fastq fastq fastq 2031302643.0 15994509.0 E MTAB 14075:Het aged S13 L001 0:8 1:28 2:91 A:398278357;C:344264985;G:353424298;T:359473296;N:59383 8 28 91   398278357 344264985 353424298 359473296 59383 ERX12481363 ERS19896180 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15625 15625 ERR13109739 ERX12481363 ERS19896180 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het aged SAMEA115618600 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het aged p Het aged p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_aged_S13_L002_I1_001.fastq.gz Het_aged_S13_L002_R1_001.fastq.gz Het_aged_S13_L002_R2_001.fastq.gz fastq fastq fastq 2430576292.0 19138396.0 E MTAB 14075:Het aged S13 L002 0:8 1:28 2:91 A:476457271;C:411953563;G:422659830;T:430445714;N:77658 8 28 91   476457271 411953563 422659830 430445714 77658 ERX12481363 ERS19896180 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15626 15626 ERR13109736 ERX12481364 ERS19896181 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het young SAMEA115618601 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het young p Het young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_young_S14_L001_I1_001.fastq.gz Het_young_S14_L001_R1_001.fastq.gz Het_young_S14_L001_R2_001.fastq.gz fastq fastq fastq 7202197051.0 56710213.0 E MTAB 14075:Het young S14 L001 0:8 1:28 2:91 A:1452033851;C:1164601809;G:1229900451;T:1313862644;N:230628 8 28 91   1452033851 1164601809 1229900451 1313862644 230628 ERX12481364 ERS19896181 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15627 15627 ERR13109740 ERX12481364 ERS19896181 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het young SAMEA115618601 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het young p Het young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_young_run2_S11_L001_I1_001.fastq.gz Het_young_run2_S11_L001_R1_001.fastq.gz Het_young_run2_S11_L001_R2_001.fastq.gz fastq fastq fastq 3012722750.0 24101782.0 E MTAB 14075:Het young run2 S11 L001 0:8 1:28 2:89 A:601664996;C:487380557;G:514748426;T:541261211;N:3408 8 28 89   601664996 487380557 514748426 541261211 3408 ERX12481364 ERS19896181 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15628 15628 ERR13109735 ERX12481364 ERS19896181 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het young SAMEA115618601 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het young p Het young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_young_run2_S11_L002_I1_001.fastq.gz Het_young_run2_S11_L002_R1_001.fastq.gz Het_young_run2_S11_L002_R2_001.fastq.gz fastq fastq fastq 3017568125.0 24140545.0 E MTAB 14075:Het young run2 S11 L002 0:8 1:28 2:89 A:602793366;C:487819335;G:515271935;T:542618728;N:5141 8 28 89   602793366 487819335 515271935 542618728 5141 ERX12481364 ERS19896181 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
15629 15629 ERR13109726 ERX12481364 ERS19896181 ERP160330 PRJEB75769 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E-MTAB-14075 Transcriptome Analysis The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. Het young SAMEA115618601 Department of Hematology cancer institute ErasmusMC ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO                 Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish E MTAB 14075:Het young p Het young p Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP160330 Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 Het_young_S14_L002_I1_001.fastq.gz Het_young_S14_L002_R1_001.fastq.gz Het_young_S14_L002_R2_001.fastq.gz fastq fastq fastq 8707482077.0 68562851.0 E MTAB 14075:Het young S14 L002 0:8 1:28 2:91 A:1755361511;C:1408255848;G:1486295783;T:1588996810;N:309489 8 28 91   1755361511 1408255848 1486295783 1588996810 309489 ERX12481364 ERS19896181 ERA30396266 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United Kingdom 2024-11-05 Adult Adult Multi-tissue Multi-system
24790 24790 SRR25509944 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz fastq fastq fastq 5999080077.0 47236851.0 GSM7680083 r1 0:8 1:28 2:91 A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071 8 28 91   1212144705 959823109 1045323833 1081182723 79071 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91673   0.11695   0.77481   0.51165   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24791 24791 SRR25509945 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz fastq fastq fastq 6012350180.0 47341340.0 GSM7680083 r2 0:8 1:28 2:91 A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064 8 28 91   1215185110 961739027 1047332997 1083733742 71064 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.11714   0.7763   0.51731   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24792 24792 SRR25509946 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz fastq fastq fastq 4990947473.0 39298799.0 GSM7680083 r3 0:8 1:28 2:91 A:1007619958;C:800073636;G:871756682;T:896670984;N:69449 8 28 91   1007619958 800073636 871756682 896670984 69449 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91717   0.11737   0.7767   0.51879   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24793 24793 SRR25509947 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz fastq fastq fastq 4994343707.0 39325541.0 GSM7680083 r4 0:8 1:28 2:91 A:1008545361;C:800479170;G:872044753;T:897494026;N:60921 8 28 91   1008545361 800479170 872044753 897494026 60921 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9173   0.11671   0.778   0.51414   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24794 24794 SRR25509948 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz fastq fastq fastq 4150807675.0 32683525.0 GSM7680083 r7 0:8 1:28 2:91 A:839301254;C:665476121;G:723277159;T:746089009;N:57232 8 28 91   839301254 665476121 723277159 746089009 57232 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91704   0.11665   0.77589   0.51231   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24795 24795 SRR25509949 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz fastq fastq fastq 4152701499.0 32698437.0 GSM7680083 r8 0:8 1:28 2:91 A:839837413;C:665793367;G:723399518;T:746476220;N:51249 8 28 91   839837413 665793367 723399518 746476220 51249 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91769   0.11677   0.77473   0.5172   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24796 24796 SRR25510006 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz fastq fastq fastq 5570139228.0 43859364.0 GSM7680083 r5 0:8 1:28 2:91 A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451 8 28 91   1124433319 892106407 974065175 1000519772 77451 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9181   0.11708   0.77725   0.506   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24797 24797 SRR25510007 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz fastq fastq fastq 5568879134.0 43849442.0 GSM7680083 r6 0:8 1:28 2:91 A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980 8 28 91   1124462080 891765530 973382320 1000621312 67980 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91836   0.11752   0.77786   0.49118   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24798 24798 SRR25509950 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz fastq fastq fastq 6472457718.0 50964234.0 GSM7680088 r1 0:8 1:28 2:91 A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737 8 28 91   1374177983 969847712 1063043909 1230585953 89737 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91899   0.23002   0.75597   0.50918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24799 24799 SRR25509951 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz fastq fastq fastq 6479801747.0 51022061.0 GSM7680088 r2 0:8 1:28 2:91 A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722 8 28 91   1375879660 970771702 1064110805 1232166662 78722 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.23011   0.75666   0.50726   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24800 24800 SRR25509952 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz fastq fastq fastq 6055044278.0 47677514.0 GSM7680088 r3 0:8 1:28 2:91 A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317 8 28 91   1285162347 907248700 995411468 1150745942 85317 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91771   0.2306   0.75799   0.51641   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24801 24801 SRR25509953 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz fastq fastq fastq 6065969453.0 47763539.0 GSM7680088 r4 0:8 1:28 2:91 A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268 8 28 91   1287814805 908939739 996849881 1152803356 74268 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91856   0.23244   0.75844   0.51273   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24802 24802 SRR25509954 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz fastq fastq fastq 5279309101.0 41569363.0 GSM7680088 r5 0:8 1:28 2:91 A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759 8 28 91   1122213686 789300425 868235888 1002988275 73759 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91638   0.23107   0.75795   0.51508   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24803 24803 SRR25509955 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz fastq fastq fastq 5282579605.0 41595115.0 GSM7680088 r6 0:8 1:28 2:91 A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051 8 28 91   1123052612 789776127 868371205 1003891470 64051 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91687   0.23155   0.75653   0.51167   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24804 24804 SRR25509956 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz fastq fastq fastq 5155833986.0 40597118.0 GSM7680088 r7 0:8 1:28 2:91 A:1096166065;C:771837218;G:846468036;T:979794053;N:72366 8 28 91   1096166065 771837218 846468036 979794053 72366 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91864   0.23062   0.75783   0.5144   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24805 24805 SRR25509957 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz fastq fastq fastq 5158852395.0 40620885.0 GSM7680088 r8 0:8 1:28 2:91 A:1096925078;C:772260867;G:846795917;T:980455576;N:63097 8 28 91   1096925078 772260867 846795917 980455576 63097 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91859   0.23143   0.75921   0.51192   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24806 24806 SRR25509958 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz fastq fastq fastq 7339736654.0 57793202.0 GSM7680087 r1 0:8 1:28 2:91 A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143 8 28 91   1557377528 1077119414 1156228317 1468352980 103143 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91516   0.25902   0.74255   0.49922   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24807 24807 SRR25509959 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz fastq fastq fastq 7410090336.0 58347168.0 GSM7680087 r2 0:8 1:28 2:91 A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640 8 28 91   1569421640 1090998538 1171253819 1477822651 95640 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91462   0.25846   0.74215   0.49672   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24808 24808 SRR25509960 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz fastq fastq fastq 7620847217.0 60006671.0 GSM7680087 r3 0:8 1:28 2:91 A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516 8 28 91   1615026295 1121044318 1201364994 1523062938 108516 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91495   0.26021   0.74188   0.49871   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24809 24809 SRR25509961 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz fastq fastq fastq 7658170739.0 60300557.0 GSM7680087 r4 0:8 1:28 2:91 A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460 8 28 91   1620018228 1130072970 1211145212 1526013817 100460 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9153   0.25733   0.74406   0.49822   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24810 24810 SRR25509962 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz fastq fastq fastq 7520150568.0 59213784.0 GSM7680087 r5 0:8 1:28 2:91 A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722 8 28 91   1592224470 1104917106 1187483622 1503722424 106722 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91528   0.25852   0.74168   0.50087   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24811 24811 SRR25509963 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz fastq fastq fastq 7547416198.0 59428474.0 GSM7680087 r6 0:8 1:28 2:91 A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676 8 28 91   1595335949 1112405532 1195632258 1504519719 97676 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91572   0.25684   0.74227   0.49429   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24812 24812 SRR25509964 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz fastq fastq fastq 6203887389.0 48849507.0 GSM7680087 r7 0:8 1:28 2:91 A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730 8 28 91   1315023626 910416020 979167464 1240610297 87730 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91294   0.25905   0.74426   0.49642   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24813 24813 SRR25509965 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz fastq fastq fastq 6164249419.0 48537397.0 GSM7680087 r8 0:8 1:28 2:91 A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064 8 28 91   1303982345 907803673 976227040 1228810005 80064 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91422   0.25666   0.74383   0.49596   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24814 24814 SRR25509966 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz fastq fastq fastq 2154821446.0 16967098.0 GSM7680086 r1 0:8 1:28 2:91 A:451330902;C:339756831;G:379343350;T:373544930;N:29905 8 28 91   451330902 339756831 379343350 373544930 29905 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91882   0.142   0.78299   0.51956   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24815 24815 SRR25509967 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz fastq fastq fastq 2158219204.0 16993852.0 GSM7680086 r2 0:8 1:28 2:91 A:452280625;C:340228509;G:379707034;T:374197697;N:26667 8 28 91   452280625 340228509 379707034 374197697 26667 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91895   0.1417   0.78279   0.51981   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24816 24816 SRR25509968 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz fastq fastq fastq 2361287251.0 18592813.0 GSM7680086 r3 0:8 1:28 2:91 A:492891294;C:373079069;G:416862992;T:409079819;N:32809 8 28 91   492891294 373079069 416862992 409079819 32809 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92068   0.13997   0.78516   0.50532   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24817 24817 SRR25509969 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz fastq fastq fastq 2362115545.0 18599335.0 GSM7680086 r4 0:8 1:28 2:91 A:493282758;C:373220256;G:416785305;T:409222388;N:28778 8 28 91   493282758 373220256 416785305 409222388 28778 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92013   0.14129   0.78468   0.52049   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24818 24818 SRR25509970 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz fastq fastq fastq 2093107066.0 16481158.0 GSM7680086 r5 0:8 1:28 2:91 A:438295698;C:330083473;G:369094473;T:362282989;N:28745 8 28 91   438295698 330083473 369094473 362282989 28745 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91759   0.13991   0.78354   0.51917   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24819 24819 SRR25509971 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz fastq fastq fastq 2095025401.0 16496263.0 GSM7680086 r6 0:8 1:28 2:91 A:438926470;C:330300198;G:369243520;T:362664613;N:25132 8 28 91   438926470 330300198 369243520 362664613 25132 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91795   0.14216   0.78151   0.5067   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24820 24820 SRR25509972 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz fastq fastq fastq 1722573390.0 13563570.0 GSM7680086 r7 0:8 1:28 2:91 A:360865837;C:272246731;G:303643951;T:297504190;N:24161 8 28 91   360865837 272246731 303643951 297504190 24161 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91897   0.13999   0.78648   0.49913   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24821 24821 SRR25509973 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz fastq fastq fastq 1724036303.0 13575089.0 GSM7680086 r8 0:8 1:28 2:91 A:361391368;C:272402118;G:303699423;T:297819212;N:20978 8 28 91   361391368 272402118 303699423 297819212 20978 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92182   0.14094   0.78326   0.50699   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24822 24822 SRR25509974 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz fastq fastq fastq 8567717053.0 67462339.0 GSM7680085 r1 0:8 1:28 2:91 A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426 8 28 91   1758073165 1341216272 1446728174 1592934812 120426 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90663   0.17669   0.75812   0.50234   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24823 24823 SRR25509975 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz fastq fastq fastq 8694310526.0 68459138.0 GSM7680085 r2 0:8 1:28 2:91 A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637 8 28 91   1780912602 1365177337 1472402153 1611176829 112637 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90543   0.17508   0.76019   0.51005   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24824 24824 SRR25509976 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz fastq fastq fastq 9112215456.0 71749728.0 GSM7680085 r3 0:8 1:28 2:91 A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116 8 28 91   1868388882 1426817380 1540502920 1693385950 130116 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90763   0.17756   0.76102   0.50457   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24825 24825 SRR25509977 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz fastq fastq fastq 9170568781.0 72209203.0 GSM7680085 r4 0:8 1:28 2:91 A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897 8 28 91   1876786596 1440704341 1555176461 1698251178 118897 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9062   0.17617   0.76203   0.49732   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24826 24826 SRR25509978 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz fastq fastq fastq 96282510.0 758130.0 GSM7680085 r5 0:8 1:28 2:91 A:19884451;C:15070058;G:16206702;T:17827293;N:1326 8 28 91   19884451 15070058 16206702 17827293 1326 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76071   0.14671   0.78064   0.49267   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24827 24827 SRR25509979 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz fastq fastq fastq 96503236.0 759868.0 GSM7680085 r6 0:8 1:28 2:91 A:19898524;C:15152212;G:16290226;T:17805918;N:1108 8 28 91   19898524 15152212 16290226 17805918 1108 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76382   0.1467   0.78508   0.48995   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24828 24828 SRR25509980 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz fastq fastq fastq 8873313978.0 69868614.0 GSM7680085 r7 0:8 1:28 2:91 A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240 8 28 91   1820893372 1390912026 1498935631 1647176605 126240 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90718   0.17603   0.76211   0.50458   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24829 24829 SRR25509981 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz fastq fastq fastq 8980314526.0 70711138.0 GSM7680085 r8 0:8 1:28 2:91 A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380 8 28 91   1839681468 1412028536 1521396962 1661490212 116380 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9078   0.17604   0.76037   0.47729   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24830 24830 SRR25509982 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz fastq fastq fastq 8634577600.0 67988800.0 GSM7680084 r1 0:8 1:28 2:91 A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058 8 28 91   1833391508 1279550998 1408086737 1665829499 122058 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92   0.2485   0.75552   0.51753   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24831 24831 SRR25509983 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz fastq fastq fastq 8644279892.0 68065196.0 GSM7680084 r2 0:8 1:28 2:91 A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347 8 28 91   1835831383 1280886675 1409188624 1667919807 106347 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91942   0.24867   0.75396   0.52058   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24832 24832 SRR25509984 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz fastq fastq fastq 6144243998.0 48379874.0 GSM7680084 r3 0:8 1:28 2:91 A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744 8 28 91   1307018689 910675193 999334562 1185454346 85744 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91944   0.2505   0.75538   0.5154   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24833 24833 SRR25509985 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz fastq fastq fastq 6161162938.0 48513094.0 GSM7680084 r4 0:8 1:28 2:91 A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675 8 28 91   1310818438 913067206 1001801994 1188928241 75675 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91847   0.24895   0.75483   0.52092   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24834 24834 SRR25509986 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz fastq fastq fastq 6893652075.0 54280725.0 GSM7680084 r5 0:8 1:28 2:91 A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988 8 28 91   1466387768 1021460104 1123606745 1327994370 96988 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92042   0.24759   0.75663   0.51662   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24835 24835 SRR25509987 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz fastq fastq fastq 6907881409.0 54392767.0 GSM7680084 r6 0:8 1:28 2:91 A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592 8 28 91   1469526451 1023529399 1125771813 1330830542 83592 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91879   0.24904   0.75479   0.52175   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24836 24836 SRR25509988 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz fastq fastq fastq 6155284362.0 48466806.0 GSM7680084 r7 0:8 1:28 2:91 A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300 8 28 91   1309788155 909805561 1001863122 1188939208 83300 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.252   0.7541   0.52096   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24837 24837 SRR25509989 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz fastq fastq fastq 6165991605.0 48551115.0 GSM7680084 r8 0:8 1:28 2:91 A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739 8 28 91   1312424825 911081786 1003163970 1191408145 72739 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.24989   0.75542   0.51918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24838 24838 SRR25509990 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz fastq fastq fastq 3327423622.0 26200186.0 GSM7680082 r1 0:8 1:28 2:91 A:693698335;C:494975421;G:540414923;T:654926705;N:201542 8 28 91   693698335 494975421 540414923 654926705 201542 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91351   0.22865   0.77723   0.49805   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24839 24839 SRR25509991 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz fastq fastq fastq 4430975390.0 34889570.0 GSM7680082 r10 0:8 1:28 2:91 A:923557751;C:658731986;G:718325003;T:874072049;N:264081 8 28 91   923557751 658731986 718325003 874072049 264081 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91797   0.22868   0.77863   0.50737   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24840 24840 SRR25509992 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz fastq fastq fastq 4429223552.0 34875776.0 GSM7680082 r11 0:8 1:28 2:91 A:923277621;C:658440918;G:718036099;T:873676803;N:264175 8 28 91   923277621 658440918 718036099 873676803 264175 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91753   0.22978   0.77942   0.50977   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24841 24841 SRR25509993 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz fastq fastq fastq 4549656890.0 35824070.0 GSM7680082 r12 0:8 1:28 2:91 A:950423951;C:673969790;G:734760168;T:900554096;N:282365 8 28 91   950423951 673969790 734760168 900554096 282365 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91687   0.23323   0.77932   0.50984   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24842 24842 SRR25509994 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz fastq fastq fastq 2696456634.0 21231942.0 GSM7680082 r13 0:8 1:28 2:91 A:562209710;C:401113540;G:437836456;T:530785441;N:161575 8 28 91   562209710 401113540 437836456 530785441 161575 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91384   0.22885   0.77912   0.50672   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24843 24843 SRR25509995 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz fastq fastq fastq 2735162932.0 21536716.0 GSM7680082 r14 0:8 1:28 2:91 A:570169460;C:406846839;G:443964376;T:538696359;N:164122 8 28 91   570169460 406846839 443964376 538696359 164122 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91691   0.22998   0.77942   0.51035   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24844 24844 SRR25509996 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz fastq fastq fastq 2739703563.0 21572469.0 GSM7680082 r15 0:8 1:28 2:91 A:571283074;C:407511119;G:444574049;T:539563747;N:162690 8 28 91   571283074 407511119 444574049 539563747 162690 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91526   0.22747   0.7793   0.51387   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24845 24845 SRR25509997 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz fastq fastq fastq 2828960433.0 22275279.0 GSM7680082 r16 0:8 1:28 2:91 A:591166850;C:419193897;G:457332081;T:559181603;N:175958 8 28 91   591166850 419193897 457332081 559181603 175958 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91651   0.23126   0.77613   0.50223   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24846 24846 SRR25509998 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz fastq fastq fastq 3374189340.0 26568420.0 GSM7680082 r2 0:8 1:28 2:91 A:703424426;C:501911907;G:547786373;T:664402117;N:201397 8 28 91   703424426 501911907 547786373 664402117 201397 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91522   0.22812   0.77753   0.50208   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24847 24847 SRR25509999 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz fastq fastq fastq 3383217516.0 26639508.0 GSM7680082 r3 0:8 1:28 2:91 A:705514047;C:503189161;G:549089218;T:666200894;N:201908 8 28 91   705514047 503189161 549089218 666200894 201908 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91535   0.23036   0.78078   0.50202   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24848 24848 SRR25510000 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz fastq fastq fastq 3493154050.0 27505150.0 GSM7680082 r4 0:8 1:28 2:91 A:729910298;C:517582902;G:564926384;T:690333365;N:215701 8 28 91   729910298 517582902 564926384 690333365 215701 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91569   0.22913   0.77873   0.50186   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24849 24849 SRR25510001 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz fastq fastq fastq 3237456187.0 25491781.0 GSM7680082 r5 0:8 1:28 2:91 A:674885196;C:481871349;G:525642933;T:637154812;N:197781 8 28 91   674885196 481871349 525642933 637154812 197781 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91378   0.22852   0.77843   0.50985   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24850 24850 SRR25510002 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz fastq fastq fastq 3287789081.0 25888103.0 GSM7680082 r6 0:8 1:28 2:91 A:685408765;C:489232060;G:533550966;T:647427897;N:197685 8 28 91   685408765 489232060 533550966 647427897 197685 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91484   0.22872   0.78001   0.49909   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24851 24851 SRR25510003 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz fastq fastq fastq 3298207145.0 25970135.0 GSM7680082 r7 0:8 1:28 2:91 A:687621787;C:490851045;G:535230137;T:649382247;N:197069 8 28 91   687621787 490851045 535230137 649382247 197069 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91559   0.2268   0.77766   0.50935   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24852 24852 SRR25510004 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz fastq fastq fastq 3377888088.0 26597544.0 GSM7680082 r8 0:8 1:28 2:91 A:705624374;C:500985504;G:546306692;T:667248332;N:211602 8 28 91   705624374 500985504 546306692 667248332 211602 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91679   0.22965   0.77837   0.51495   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
24853 24853 SRR25510005 SRX21240518 SRS18495441 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed 2dpf scRNAseq GSM7680082   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed 2dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs GSM7680082 GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq GSM7680082 r1 GSM7680082 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz fastq fastq fastq 4346114117.0 34221371.0 GSM7680082 r9 0:8 1:28 2:91 A:905838814;C:646261347;G:704993570;T:856789016;N:262014 8 28 91   905838814 646261347 704993570 856789016 262014 SRX21240518 SRS18495441 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91558   0.22834   0.7783   0.49972   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Hatching Embryo Tail Multi-system
25133 25133 SRR25634296 SRX21361065 SRS18605555 SRP454944 PRJNA1005241 Nkx2.7 is a Conserved Regulator of Craniofacial Development GSE240780 Transcriptome Analysis Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.   pubmed:40268889   KC002 scRNAseq GSM7709162   source name:Pharyngeal arches|genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing KC002 scRNAseq The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files Pharyngeal arches   From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf GSM7709162 GSM7709162: KC002 scRNAseq; Danio rerio; RNA Seq GSM7709162 r1 GSM7709162 1 From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454944   loader:fastq load.py|options: readTypes=TTBB read1PairFiles=KC002 S1 L004 I1 001.fastq.gz read2PairFiles=KC002 S1 L004 I2 001.fastq.gz read3PairFiles=KC002 S1 L004 R1 001.fastq.gz read4PairFiles=KC002 S1 L004 R2 001.fastq.gz KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz fastq fastq fastq fastq 65825988564.0 296513462.0 GSM7709162 r1 0:10 1:10 2:101 3:101 A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035 10 10 101 101 14990994149 11485312838 11921291570 21497933732 187035 SRX21361065 SRS18605555 SRA1692494 SangesLab Computational Genomics, NEUROSCIENCE, SISSA SangesLab Computational Genomics, NEUROSCIENCE, SISSA 2 0.00059 0.93473 2e-05 0.14487 0.99949 0.78364 0.5 0.52799 101 101 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Italy 2023-08-14 Pharyngula Embryo Pharyngeal Arch Multi-system
25134 25134 SRR25634297 SRX21361064 SRS18605556 SRP454944 PRJNA1005241 Nkx2.7 is a Conserved Regulator of Craniofacial Development GSE240780 Transcriptome Analysis Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.   pubmed:40268889   KC001 scRNAseq GSM7709161   source name:Pharyngeal arches|genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing KC001 scRNAseq The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files Pharyngeal arches   From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf GSM7709161 GSM7709161: KC001 scRNAseq; Danio rerio; RNA Seq GSM7709161 r1 GSM7709161 1 From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454944   loader:fastq load.py|options: readTypes=TTBB read1PairFiles=KC001 S1 L004 I1 001.fastq.gz read2PairFiles=KC001 S1 L004 I2 001.fastq.gz read3PairFiles=KC001 S1 L004 R1 001.fastq.gz read4PairFiles=KC001 S1 L004 R2 001.fastq.gz KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz fastq fastq fastq fastq 69380677872.0 312525576.0 GSM7709161 r1 0:10 1:10 2:101 3:101 A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567 10 10 101 101 16018222868 11704492905 12161620273 23245625739 204567 SRX21361064 SRS18605556 SRA1692494 SangesLab Computational Genomics, NEUROSCIENCE, SISSA SangesLab Computational Genomics, NEUROSCIENCE, SISSA 2 0.00071 0.93976 0.0001 0.12725 0.99945 0.78457 0.75 0.50121 101 101 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Italy 2023-08-14 Pharyngula Embryo Pharyngeal Arch Multi-system
25237 25237 SRR25721801 SRX21445937 SRS18680715 SRP456253 PRJNA1007646 Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva] GSE241296 Other Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration…       zebrafish larva neurons and glia scRNAseq GSM7720759   source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing zebrafish larva neurons and glia scRNAseq using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files zebrafish larva   About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.   cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf GSM7720759 GSM7720759: zebrafish larva neurons and glia scRNAseq; Danio rerio; RNA Seq GSM7720759 r1 GSM7720759 1 About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456253   loader:fastq load.py CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz fastq fastq fastq fastq 55936355640.0 254256162.0 GSM7720759 r1 0:10 1:10 2:100 3:100 A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132 10 10 100 100 13207297968 10496996981 10989402500 16156355819 1179132 SRX21445937 SRS18680715 SRA1696793 Oregon Health and Science Univ Oregon Health and Science Univ 2 0.0 0.81961 0.0 0.19165 1.0 0.8508   0.59575 100 100 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-21 Larval Larval Multi-tissue Multi-system
25238 25238 SRR25721802 SRX21445937 SRS18680715 SRP456253 PRJNA1007646 Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva] GSE241296 Other Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration…       zebrafish larva neurons and glia scRNAseq GSM7720759   source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing zebrafish larva neurons and glia scRNAseq using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files zebrafish larva   About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.   cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf GSM7720759 GSM7720759: zebrafish larva neurons and glia scRNAseq; Danio rerio; RNA Seq GSM7720759 r1 GSM7720759 1 About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456253   loader:fastq load.py CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 54474841080.0 247612914.0 GSM7720759 r2 0:10 1:10 2:100 3:100 A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834 10 10 100 100 12887048507 10210716068 10683375130 15740176261 1266834 SRX21445937 SRS18680715 SRA1696793 Oregon Health and Science Univ Oregon Health and Science Univ 2 0.0 0.82189 0.0 0.19349 1.0 0.85025   0.6092 100 100 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-21 Larval Larval Multi-tissue Multi-system
28707 28707 SRR26588119 SRX22289209 SRS19340293 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 5.8 mm GSM7871949   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 5.8 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871949 GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq GSM7871949 r1 GSM7871949 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0628_S3_L001_R2_001.fastq.gz FS_WT0628_S3_L001_R1_001.fastq.gz FS_WT0628_S3_L001_I1_001.fastq.gz fastq fastq fastq 3515731348.0 27682924.0 GSM7871949 r1 0:8 1:28 2:91 A:723968955;C:551528974;G:650193733;T:593113624;N:340798 8 28 91   723968955 551528974 650193733 593113624 340798 SRX22289209 SRS19340293 SRA1742079 Boston University Boston University 1 0.8674   0.17534   0.84098   0.62971   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28708 28708 SRR26588120 SRX22289209 SRS19340293 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 5.8 mm GSM7871949   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 5.8 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871949 GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq GSM7871949 r1 GSM7871949 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0628_S3_L002_R2_001.fastq.gz FS_WT0628_S3_L002_R1_001.fastq.gz FS_WT0628_S3_L002_I1_001.fastq.gz fastq fastq fastq 3453128095.0 27189985.0 GSM7871949 r2 0:8 1:28 2:91 A:711376907;C:541911169;G:638181451;T:582510928;N:308180 8 28 91   711376907 541911169 638181451 582510928 308180 SRX22289209 SRS19340293 SRA1742079 Boston University Boston University 1 0.86684   0.17663   0.84108   0.64294   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28709 28709 SRR26588121 SRX22289209 SRS19340293 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 5.8 mm GSM7871949   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 5.8 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871949 GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq GSM7871949 r1 GSM7871949 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0628_S3_L003_R2_001.fastq.gz FS_WT0628_S3_L003_R1_001.fastq.gz FS_WT0628_S3_L003_I1_001.fastq.gz fastq fastq fastq 3525654366.0 27761058.0 GSM7871949 r3 0:8 1:28 2:91 A:725811733;C:554304351;G:651619754;T:593988032;N:532408 8 28 91   725811733 554304351 651619754 593988032 532408 SRX22289209 SRS19340293 SRA1742079 Boston University Boston University 1 0.86621   0.17459   0.83936   0.63657   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28710 28710 SRR26588122 SRX22289209 SRS19340293 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 5.8 mm GSM7871949   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 5.8 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871949 GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq GSM7871949 r1 GSM7871949 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0628_S3_L004_R2_001.fastq.gz FS_WT0628_S3_L004_R1_001.fastq.gz FS_WT0628_S3_L004_I1_001.fastq.gz fastq fastq fastq 3476431706.0 27373478.0 GSM7871949 r4 0:8 1:28 2:91 A:715940083;C:546111535;G:642639757;T:585816460;N:478663 8 28 91   715940083 546111535 642639757 585816460 478663 SRX22289209 SRS19340293 SRA1742079 Boston University Boston University 1 0.86857   0.17561   0.84094   0.63847   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28711 28711 SRR26588123 SRX22289208 SRS19340290 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 7.0 mm GSM7871948   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 7.0 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871948 GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq GSM7871948 r1 GSM7871948 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0621_S1_L001_R2_001.fastq.gz FS_WT0621_S1_L001_R1_001.fastq.gz FS_WT0621_S1_L001_I1_001.fastq.gz fastq fastq fastq 4296091865.0 33827495.0 GSM7871948 r1 0:8 1:28 2:91 A:873692918;C:671758488;G:778592608;T:753844494;N:413537 8 28 91   873692918 671758488 778592608 753844494 413537 SRX22289208 SRS19340290 SRA1742079 Boston University Boston University 1 0.88226   0.23142   0.80811   0.58869   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28712 28712 SRR26588124 SRX22289208 SRS19340290 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 7.0 mm GSM7871948   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 7.0 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871948 GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq GSM7871948 r1 GSM7871948 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0621_S1_L002_R2_001.fastq.gz FS_WT0621_S1_L002_R1_001.fastq.gz FS_WT0621_S1_L002_I1_001.fastq.gz fastq fastq fastq 4219879546.0 33227398.0 GSM7871948 r2 0:8 1:28 2:91 A:858665689;C:660231321;G:764062561;T:740359496;N:374151 8 28 91   858665689 660231321 764062561 740359496 374151 SRX22289208 SRS19340290 SRA1742079 Boston University Boston University 1 0.8833   0.23028   0.80734   0.5998   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-system
28713 28713 SRR26588125 SRX22289208 SRS19340290 SRP469198 PRJNA1033661 scRNAseq of skeletal tissue during zebrafish craniofacial development GSE246579 Transcriptome Analysis We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation and compared wildtype fish to mutants lacking the transcription factor sp7 that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at 5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues brain and eyes were removed before dissociation. To aid in dissection and transcript analysis fish carried two transgenes 117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.       WT 7.0 mm GSM7871948   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing WT 7.0 mm Demultiplexing barcoded processing gene counting and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files craniofacial skeletal tissues   Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   tissue:craniofacial skeletal tissues|genotype:WT GSM7871948 GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq GSM7871948 r1 GSM7871948 1 Fish were euthanized and transferred to ice cold PBS. In <2 min we cut off the head just above the pectoral fins and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30° the tissue was fully dissociated again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min cells were resuspended in PBS centrifuged again to wash and the final pellet resuspended in 100μL of FACS buffer 1x PBS 2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP469198   loader:fastq load.py FS_WT0621_S1_L003_R2_001.fastq.gz FS_WT0621_S1_L003_R1_001.fastq.gz FS_WT0621_S1_L003_I1_001.fastq.gz fastq fastq fastq 4341378795.0 34184085.0 GSM7871948 r3 0:8 1:28 2:91 A:882850653;C:681021491;G:786172206;T:760063970;N:643415 8 28 91   882850653 681021491 786172206 760063970 643415 SRX22289208 SRS19340290 SRA1742079 Boston University Boston University 1 0.88158   0.23138   0.80921   0.5997   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-10-30 Undetermined Undetermined Multi-tissue Multi-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");;