RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

208 rows where technology = "10x" and tissue_curation = "Multi-tissue"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation 6

experiment.library_selection 5

devstage_curation_coarse 4

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 208 ✖

technology 1

  • 10x · 208 ✖

experiment.platform 1

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
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
28714 28714 SRR26588126 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_L004_R2_001.fastq.gz FS_WT0621_S1_L004_R1_001.fastq.gz FS_WT0621_S1_L004_I1_001.fastq.gz fastq fastq fastq 4270514446.0 33626098.0 GSM7871948 r4 0:8 1:28 2:91 A:868634109;C:669284353;G:773305808;T:748175261;N:575387 8 28 91   868634109 669284353 773305808 748175261 575387 SRX22289208 SRS19340290 SRA1742079 Boston University Boston University 1 0.8822   0.23032   0.80695   0.58745   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
28715 28715 SRR26588127 SRX22289207 SRS19340289 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.       sp7 mutant 5.8 mm GSM7871947   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871947 GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq GSM7871947 r1 GSM7871947 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_Mutant0628_S4_L001_R2_001.fastq.gz FS_Mutant0628_S4_L001_R1_001.fastq.gz FS_Mutant0628_S4_L001_I1_001.fastq.gz fastq fastq fastq 3870633229.0 30477427.0 GSM7871947 r1 0:8 1:28 2:91 A:784323459;C:609892390;G:730737771;T:648119651;N:372586 8 28 91   784323459 609892390 730737771 648119651 372586 SRX22289207 SRS19340289 SRA1742079 Boston University Boston University 1 0.83967   0.19678   0.84027   0.62798   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
28716 28716 SRR26588128 SRX22289207 SRS19340289 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.       sp7 mutant 5.8 mm GSM7871947   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871947 GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq GSM7871947 r1 GSM7871947 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_Mutant0628_S4_L002_R2_001.fastq.gz FS_Mutant0628_S4_L002_R1_001.fastq.gz FS_Mutant0628_S4_L002_I1_001.fastq.gz fastq fastq fastq 3795705896.0 29887448.0 GSM7871947 r2 0:8 1:28 2:91 A:769584134;C:598310890;G:715720368;T:635803045;N:339331 8 28 91   769584134 598310890 715720368 635803045 339331 SRX22289207 SRS19340289 SRA1742079 Boston University Boston University 1 0.83992   0.199   0.84094   0.63528   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
28717 28717 SRR26588129 SRX22289207 SRS19340289 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.       sp7 mutant 5.8 mm GSM7871947   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871947 GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq GSM7871947 r1 GSM7871947 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_Mutant0628_S4_L003_I1_001.fastq.gz FS_Mutant0628_S4_L003_R1_001.fastq.gz FS_Mutant0628_S4_L003_R2_001.fastq.gz fastq fastq fastq 3882075802.0 30567526.0 GSM7871947 r3 0:8 1:28 2:91 A:786373431;C:613286785;G:731993747;T:649408434;N:582469 8 28 91   786373431 613286785 731993747 649408434 582469 SRX22289207 SRS19340289 SRA1742079 Boston University Boston University 1 0.83867   0.19884   0.83826   0.63213   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
28718 28718 SRR26588130 SRX22289207 SRS19340289 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.       sp7 mutant 5.8 mm GSM7871947   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871947 GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq GSM7871947 r1 GSM7871947 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_Mutant0628_S4_L004_R2_001.fastq.gz FS_Mutant0628_S4_L004_R1_001.fastq.gz FS_Mutant0628_S4_L004_I1_001.fastq.gz fastq fastq fastq 3821331575.0 30089225.0 GSM7871947 r4 0:8 1:28 2:91 A:774445827;C:603171063;G:720511073;T:639476444;N:515068 8 28 91   774445827 603171063 720511073 639476444 515068 SRX22289207 SRS19340289 SRA1742079 Boston University Boston University 1 0.84008   0.19754   0.84076   0.63418   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
28719 28719 SRR26588131 SRX22289206 SRS19340291 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.       sp7 mutant 7.0 mm GSM7871946   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871946 GSM7871946: sp7 mutant 7.0 mm; Danio rerio; RNA Seq GSM7871946 r1 GSM7871946 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_Mutant0621_S2_L001_I1_001.fastq.gz FS_Mutant0621_S2_L001_R1_001.fastq.gz FS_Mutant0621_S2_L001_R2_001.fastq.gz fastq fastq fastq 4256651761.0 33516943.0 GSM7871946 r1 0:8 1:28 2:91 A:862245132;C:673711733;G:766388204;T:747287820;N:408924 8 28 91   862245132 673711733 766388204 747287820 408924 SRX22289206 SRS19340291 SRA1742079 Boston University Boston University 1 0.89937   0.20157   0.80691   0.60147   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
28720 28720 SRR26588132 SRX22289206 SRS19340291 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.       sp7 mutant 7.0 mm GSM7871946   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871946 GSM7871946: sp7 mutant 7.0 mm; Danio rerio; RNA Seq GSM7871946 r1 GSM7871946 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_Mutant0621_S2_L002_I1_001.fastq.gz FS_Mutant0621_S2_L002_R1_001.fastq.gz FS_Mutant0621_S2_L002_R2_001.fastq.gz fastq fastq fastq 4173795437.0 32864531.0 GSM7871946 r2 0:8 1:28 2:91 A:846056609;C:660910650;G:750849639;T:732486246;N:369177 8 28 91   846056609 660910650 750849639 732486246 369177 SRX22289206 SRS19340291 SRA1742079 Boston University Boston University 1 0.89896   0.20107   0.80415   0.60881   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
28721 28721 SRR26588133 SRX22289206 SRS19340291 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.       sp7 mutant 7.0 mm GSM7871946   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871946 GSM7871946: sp7 mutant 7.0 mm; Danio rerio; RNA Seq GSM7871946 r1 GSM7871946 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_Mutant0621_S2_L003_I1_001.fastq.gz FS_Mutant0621_S2_L003_R1_001.fastq.gz FS_Mutant0621_S2_L003_R2_001.fastq.gz fastq fastq fastq 4291089081.0 33788103.0 GSM7871946 r3 0:8 1:28 2:91 A:869084749;C:681276277;G:772278057;T:751443489;N:634801 8 28 91   869084749 681276277 772278057 751443489 634801 SRX22289206 SRS19340291 SRA1742079 Boston University Boston University 1 0.89995   0.20079   0.80505   0.60752   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
28722 28722 SRR26588134 SRX22289206 SRS19340291 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.       sp7 mutant 7.0 mm GSM7871946   source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing sp7 mutant 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:sp7 / GSM7871946 GSM7871946: sp7 mutant 7.0 mm; Danio rerio; RNA Seq GSM7871946 r1 GSM7871946 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_Mutant0621_S2_L004_I1_001.fastq.gz FS_Mutant0621_S2_L004_R1_001.fastq.gz FS_Mutant0621_S2_L004_R2_001.fastq.gz fastq fastq fastq 4221057598.0 33236674.0 GSM7871946 r4 0:8 1:28 2:91 A:855377679;C:669535108;G:759458317;T:739600774;N:565456 8 28 91   855377679 669535108 759458317 739600774 565456 SRX22289206 SRS19340291 SRA1742079 Boston University Boston University 1 0.90012   0.20095   0.80562   0.60729   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
29808 29808 SRR27450807 SRX23122487 SRS20076037 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf Aktmutant GSM8004755   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing Zebrafish EC 24hpf Aktmutant The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant GSM8004755 GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq GSM8004755 r1 GSM8004755 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz fastq fastq fastq 23281472741.0 183318683.0 GSM8004755 r1 0:8 1:28 2:91 A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871 8 28 91   4703583066 3702175361 3998796644 4271932211 5512871 SRX23122487 SRS20076037 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29809 29809 SRR27450808 SRX23122487 SRS20076037 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf Aktmutant GSM8004755   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing Zebrafish EC 24hpf Aktmutant The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant GSM8004755 GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq GSM8004755 r1 GSM8004755 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz fastq fastq fastq 21009317138.0 165427694.0 GSM8004755 r2 0:8 1:28 2:91 A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364 8 28 91   4231955850 3363548064 3603913589 3849411287 5091364 SRX23122487 SRS20076037 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29810 29810 SRR27450809 SRX23122486 SRS20076036 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf WT GSM8004754   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing Zebrafish EC 24hpf WT The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT GSM8004754 GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq GSM8004754 r1 GSM8004754 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz fastq fastq fastq 22261273232.0 175285616.0 GSM8004754 r1 0:8 1:28 2:91 A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557 8 28 91   4475749188 3578353646 3836029871 4055646794 5211557 SRX23122486 SRS20076036 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29811 29811 SRR27450810 SRX23122486 SRS20076036 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf WT GSM8004754   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing Zebrafish EC 24hpf WT The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT GSM8004754 GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq GSM8004754 r1 GSM8004754 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz fastq fastq fastq 20084395188.0 158144844.0 GSM8004754 r2 0:8 1:28 2:91 A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115 8 28 91   4028678970 3250176957 3455600305 3651884457 4840115 SRX23122486 SRS20076036 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29812 29812 SRR27466771 SRX23138319 SRS20089385 SRP482605 PRJNA1062705 Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation GSE252788 Transcriptome Analysis Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized which limits their applicability to studying human disease. Here we show by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors including C/ebp ß which is important for late neutrophil maturation. Cross species comparison of zebrafish mouse and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult six mpf male zebrafish was isolated labelled using lipid tagged following MULTI seq protocol for scRNA seq using 10x Genomics.   pubmed:38413586   MF317 A2 GEX zebrafish multiseq GSM8007850   source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing MF317 A2 GEX zebrafish multiseq We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object Kidney marrow   Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.   tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs GSM8007850 GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq GSM8007850 r1 GSM8007850 1 Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer's protocols 10x Genomics and sequenced by protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP482605   loader:fastq load.py MF317_A2_GEX_zebrafish_multiseq_S3_L004_I1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R2_001.fastq.gz fastq fastq fastq 20397464955.0 151092333.0 GSM8007850 r1 0:8 1:29 2:98 A:4317555978;C:3264550330;G:3319063129;T:3903632022;N:2247175 8 29 98   4317555978 3264550330 3319063129 3903632022 2247175 SRX23138319 SRS20089385     Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Austria 2024-01-09 Undetermined Adult Multi-tissue Multi-system
29813 29813 SRR27466772 SRX23138319 SRS20089385 SRP482605 PRJNA1062705 Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation GSE252788 Transcriptome Analysis Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized which limits their applicability to studying human disease. Here we show by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors including C/ebp ß which is important for late neutrophil maturation. Cross species comparison of zebrafish mouse and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult six mpf male zebrafish was isolated labelled using lipid tagged following MULTI seq protocol for scRNA seq using 10x Genomics.   pubmed:38413586   MF317 A2 GEX zebrafish multiseq GSM8007850   source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing MF317 A2 GEX zebrafish multiseq We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object Kidney marrow   Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.   tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs GSM8007850 GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq GSM8007850 r1 GSM8007850 1 Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer's protocols 10x Genomics and sequenced by protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP482605   loader:fastq load.py MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_I1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R2_001.fastq.gz fastq fastq fastq 609557670.0 4515242.0 GSM8007850 r2 0:8 1:29 2:98 A:288037892;C:47138905;G:85961330;T:21289087;N:66502 8 29 98   288037892 47138905 85961330 21289087 66502 SRX23138319 SRS20089385     Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Austria 2024-01-09 Undetermined Adult Multi-tissue Multi-system
29814 29814 SRR27466773 SRX23138318 SRS20089387 SRP482605 PRJNA1062705 Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation GSE252788 Transcriptome Analysis Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized which limits their applicability to studying human disease. Here we show by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors including C/ebp ß which is important for late neutrophil maturation. Cross species comparison of zebrafish mouse and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult six mpf male zebrafish was isolated labelled using lipid tagged following MULTI seq protocol for scRNA seq using 10x Genomics.   pubmed:38413586   MF317 A1 GEX zebrafish multiseq GSM8007849   source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing MF317 A1 GEX zebrafish multiseq We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object Kidney marrow   Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.   tissue:Kidney marrow|cell type:Neutrophils GSM8007849 GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq GSM8007849 r1 GSM8007849 1 Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer's protocols 10x Genomics and sequenced by protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP482605   loader:fastq load.py MF317_A1_GEX_zebrafish_multiseq_S1_L004_I1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R2_001.fastq.gz fastq fastq fastq 20471343840.0 151639584.0 GSM8007849 r1 0:8 1:29 2:98 A:4574898668;C:2902052527;G:3115258212;T:4266202403;N:2267422 8 29 98   4574898668 2902052527 3115258212 4266202403 2267422 SRX23138318 SRS20089387     Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Austria 2024-01-09 Undetermined Adult Multi-tissue Multi-system
29815 29815 SRR27466774 SRX23138318 SRS20089387 SRP482605 PRJNA1062705 Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation GSE252788 Transcriptome Analysis Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized which limits their applicability to studying human disease. Here we show by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors including C/ebp ß which is important for late neutrophil maturation. Cross species comparison of zebrafish mouse and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult six mpf male zebrafish was isolated labelled using lipid tagged following MULTI seq protocol for scRNA seq using 10x Genomics.   pubmed:38413586   MF317 A1 GEX zebrafish multiseq GSM8007849   source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing MF317 A1 GEX zebrafish multiseq We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object Kidney marrow   Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.   tissue:Kidney marrow|cell type:Neutrophils GSM8007849 GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq GSM8007849 r1 GSM8007849 1 Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer's protocols 10x Genomics and sequenced by protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP482605   loader:fastq load.py MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_I1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R2_001.fastq.gz fastq fastq fastq 205092135.0 1519201.0 GSM8007849 r2 0:8 1:29 2:98 A:96315447;C:12651302;G:31425404;T:8467378;N:22167 8 29 98   96315447 12651302 31425404 8467378 22167 SRX23138318 SRS20089387     Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Austria 2024-01-09 Undetermined Adult Multi-tissue Multi-system
33900 33900 SRR30879294 SRX26276609 SRS22814231 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ TKO 4 dpf GSM8553899   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing dsRED+ TKO 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO GSM8553899 GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq GSM8553899 r1 GSM8553899 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py TKO_dsRED_S2_L001_I1_001.fastq.gz TKO_dsRED_S2_L001_I2_001.fastq.gz TKO_dsRED_S2_L001_R1_001.fastq.gz TKO_dsRED_S2_L001_R2_001.fastq.gz fastq fastq fastq fastq 3764848932.0 27281514.0 GSM8553899 r1 0:10 1:10 2:28 3:90 A:692470222;C:567540605;G:576111845;T:618305574;N:908014 10 10 28 90 692470222 567540605 576111845 618305574 908014 SRX26276609 SRS22814231 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33901 33901 SRR30879295 SRX26276609 SRS22814231 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ TKO 4 dpf GSM8553899   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing dsRED+ TKO 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO GSM8553899 GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq GSM8553899 r1 GSM8553899 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py TKO_dsRED_S2_L002_I1_001.fastq.gz TKO_dsRED_S2_L002_I2_001.fastq.gz TKO_dsRED_S2_L002_R1_001.fastq.gz TKO_dsRED_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 3726674544.0 27004888.0 GSM8553899 r2 0:10 1:10 2:28 3:90 A:685914766;C:561837246;G:569990126;T:611748773;N:949009 10 10 28 90 685914766 561837246 569990126 611748773 949009 SRX26276609 SRS22814231 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33902 33902 SRR30879296 SRX26276609 SRS22814231 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ TKO 4 dpf GSM8553899   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing dsRED+ TKO 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO GSM8553899 GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq GSM8553899 r1 GSM8553899 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py TKO_dsRED_S2_L003_I1_001.fastq.gz TKO_dsRED_S2_L003_I2_001.fastq.gz TKO_dsRED_S2_L003_R1_001.fastq.gz TKO_dsRED_S2_L003_R2_001.fastq.gz fastq fastq fastq fastq 3722937918.0 26977811.0 GSM8553899 r3 0:10 1:10 2:28 3:90 A:676537253;C:555568581;G:563937331;T:604713745;N:27246080 10 10 28 90 676537253 555568581 563937331 604713745 27246080 SRX26276609 SRS22814231 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33903 33903 SRR30879297 SRX26276609 SRS22814231 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ TKO 4 dpf GSM8553899   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing dsRED+ TKO 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO GSM8553899 GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq GSM8553899 r1 GSM8553899 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py TKO_dsRED_S2_L004_I1_001.fastq.gz TKO_dsRED_S2_L004_I2_001.fastq.gz TKO_dsRED_S2_L004_R1_001.fastq.gz TKO_dsRED_S2_L004_R2_001.fastq.gz fastq fastq fastq fastq 3758183394.0 27233213.0 GSM8553899 r4 0:10 1:10 2:28 3:90 A:692108990;C:566665777;G:574900426;T:617012755;N:301222 10 10 28 90 692108990 566665777 574900426 617012755 301222 SRX26276609 SRS22814231 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33904 33904 SRR30879298 SRX26276608 SRS22814230 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ WT 4 dpf GSM8553898   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain|geo loc name:missing|collection date:missing dsRED+ WT 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain GSM8553898 GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq GSM8553898 r1 GSM8553898 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py WT_dsRED_S1_L001_I1_001.fastq.gz WT_dsRED_S1_L001_I2_001.fastq.gz WT_dsRED_S1_L001_R1_001.fastq.gz WT_dsRED_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 4039025952.0 29268304.0 GSM8553898 r1 0:10 1:10 2:28 3:90 A:743074639;C:613897517;G:610150022;T:666064959;N:960223 10 10 28 90 743074639 613897517 610150022 666064959 960223 SRX26276608 SRS22814230 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33905 33905 SRR30879299 SRX26276608 SRS22814230 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ WT 4 dpf GSM8553898   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain|geo loc name:missing|collection date:missing dsRED+ WT 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain GSM8553898 GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq GSM8553898 r1 GSM8553898 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py WT_dsRED_S1_L002_I1_001.fastq.gz WT_dsRED_S1_L002_I2_001.fastq.gz WT_dsRED_S1_L002_R1_001.fastq.gz WT_dsRED_S1_L002_R2_001.fastq.gz fastq fastq fastq fastq 3995500476.0 28952902.0 GSM8553898 r2 0:10 1:10 2:28 3:90 A:735710467;C:607339644;G:603122849;T:658578339;N:1009881 10 10 28 90 735710467 607339644 603122849 658578339 1009881 SRX26276608 SRS22814230 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33906 33906 SRR30879300 SRX26276608 SRS22814230 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ WT 4 dpf GSM8553898   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain|geo loc name:missing|collection date:missing dsRED+ WT 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain GSM8553898 GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq GSM8553898 r1 GSM8553898 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py WT_dsRED_S1_L003_I1_001.fastq.gz WT_dsRED_S1_L003_I2_001.fastq.gz WT_dsRED_S1_L003_R1_001.fastq.gz WT_dsRED_S1_L003_R2_001.fastq.gz fastq fastq fastq fastq 3989006196.0 28905842.0 GSM8553898 r3 0:10 1:10 2:28 3:90 A:725297656;C:600094089;G:596392169;T:650543321;N:29198545 10 10 28 90 725297656 600094089 596392169 650543321 29198545 SRX26276608 SRS22814230 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
33907 33907 SRR30879301 SRX26276608 SRS22814230 SRP536515 PRJNA1168532 scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf GSE278733 Transcriptome Analysis The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.       dsRED+ WT 4 dpf GSM8553898   tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain|geo loc name:missing|collection date:missing dsRED+ WT 4 dpf Following sequencing an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files 4 dpf   WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT EK strain GSM8553898 GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq GSM8553898 r1 GSM8553898 1 WT and TKO embryos were collected at 4 dpf and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP536515   loader:fastq load.py WT_dsRED_S1_L004_I1_001.fastq.gz WT_dsRED_S1_L004_I2_001.fastq.gz WT_dsRED_S1_L004_R1_001.fastq.gz WT_dsRED_S1_L004_R2_001.fastq.gz fastq fastq fastq fastq 4028525946.0 29192217.0 GSM8553898 r4 0:10 1:10 2:28 3:90 A:742291215;C:612398679;G:608091658;T:664191759;N:326219 10 10 28 90 742291215 612398679 608091658 664191759 326219 SRX26276608 SRS22814230 SRA1985700 nih nih                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-10-03 Larval Larval Multi-tissue Multi-system
43987 43987 SRR6811828 SRX3768868 SRS3023414 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 exo scar GSM3032171   source name:Pancreas except primary islet liver|strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult Pancreas 3 exo scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Pancreas except primary islet liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult GSM3032171 GSM3032171: Pancreas 3 exo scar; Danio rerio; OTHER GSM3032171   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032171 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     P7exo_scar_R1.fastq.gz P7exo_scar_R2.fastq.gz fastq fastq 4291410352.0 34608148.0 GSM3032171 r1 0:26 1:98 A:1266869162;C:1345773385;G:950601988;T:726078376;N:2087441 26 98     1266869162 1345773385 950601988 726078376 2087441 SRX3768868 SRS3023414 SRA623333 GEO Max Delbrück Center 2 0.00014 0.00241 0.00012 0.00024 0.99995 0.99691 0.0 0.65306 26 98 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Multi-tissue Multi-system
43989 43989 SRR6811826 SRX3768866 SRS3023382 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 3 scar GSM3032169   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 3 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM3032169 GSM3032169: Heart 3 scar; Danio rerio; OTHER GSM3032169   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032169 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     H7_scar_R1.fastq.gz H7_scar_R2.fastq.gz fastq fastq 3999397296.0 32253204.0 GSM3032169 r1 0:26 1:98 A:1170970784;C:1255843391;G:881154893;T:689473188;N:1955040 26 98     1170970784 1255843391 881154893 689473188 1955040 SRX3768866 SRS3023382 SRA623333 GEO Max Delbrück Center 2 0.00018 0.00228 0.00015 0.00019 0.99991 0.99659 0.8 0.67235 26 98 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Multi-tissue Multi-system
43993 43993 SRR6811822 SRX3768862 SRS3023379 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 exo mRNA GSM3032165   source name:Pancreas except primary islet liver|strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult Pancreas 3 exo mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Pancreas except primary islet liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult GSM3032165 GSM3032165: Pancreas 3 exo mRNA; Danio rerio; RNA Seq GSM3032165   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032165 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     P7exo_wt_R1.fastq.gz P7exo_wt_R2.fastq.gz fastq fastq 38574026764.0 311080861.0 GSM3032165 r1 0:26 1:98 A:10751580091;C:8744299142;G:9264760851;T:9795905887;N:17480793 26 98     10751580091 8744299142 9264760851 9795905887 17480793 SRX3768862 SRS3023379 SRA623333 GEO Max Delbrück Center 2 0.00463 0.93239 0.00336 0.04555 0.99671 0.87207 0.46341 0.57662 26 98 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Multi-tissue Multi-system
43995 43995 SRR6811820 SRX3768860 SRS3023377 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 3 mRNA GSM3032163   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 3 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM3032163 GSM3032163: Heart 3 mRNA; Danio rerio; RNA Seq GSM3032163   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032163 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     H7_wt_R2.fastq.gz H7_wt_R1.fastq.gz fastq fastq 45826897248.0 369571752.0 GSM3032163 r1 0:26 1:98 A:12856871948;C:10721924215;G:10335821801;T:11891517482;N:20761802 26 98     12856871948 10721924215 10335821801 11891517482 20761802 SRX3768860 SRS3023377 SRA623333 GEO Max Delbrück Center 2 0.00303 0.90293 0.00206 0.05991 0.99746 0.86918 0.3421 0.66847 26 98 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Multi-tissue Multi-system
44000 44000 SRR6211492 SRX3320767 SRS2626340 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 2 mRNA GSM2830062   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 2 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM2830062 GSM2830062: Heart 2 mRNA; Danio rerio; RNA Seq GSM2830062   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830062 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     H6_wt_R2.fastq.gz H6_wt_R1.fastq.gz fastq fastq 19466673438.0 141062851.0 GSM2830062 r1 0:28 1:110 A:5788453893;C:4266605110;G:4479895656;T:4930437501;N:1281278 28 110     5788453893 4266605110 4479895656 4930437501 1281278 SRX3320767 SRS2626340 SRA623333 GEO Max Delbrück Center 2 0.00114 0.94531 0.00026 0.06835 0.99819 0.88308 0.68098 0.70993 28 110 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44001 44001 SRR6211491 SRX3320766 SRS2626339 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 2 mRNA GSM2830061   source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult Pancreas 2 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Pancreas and liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult GSM2830061 GSM2830061: Pancreas 2 mRNA; Danio rerio; RNA Seq GSM2830061   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     P6_wt_R1.fastq.gz P6_wt_R2.fastq.gz fastq fastq 17563278078.0 127270131.0 GSM2830061 r1 0:28 1:110 A:5146142876;C:3830859355;G:4368254000;T:4216873712;N:1148135 28 110     5146142876 3830859355 4368254000 4216873712 1148135 SRX3320766 SRS2626339 SRA623333 GEO Max Delbrück Center 2 0.0023 0.93516 0.00062 0.07613 0.99667 0.8798 0.62666 0.6399 28 110 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44002 44002 SRR6211490 SRX3320765 SRS2626338 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 1 mRNA GSM2830060   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 1 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM2830060 GSM2830060: Heart 1 mRNA; Danio rerio; RNA Seq GSM2830060   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830060 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     H5_wt_R1.fastq.gz H5_wt_R2.fastq.gz fastq fastq 11175332616.0 88693116.0 GSM2830060 r1 0:26 1:100 A:3373517159;C:2470603501;G:2531314673;T:2798372007;N:1525276 26 100     3373517159 2470603501 2531314673 2798372007 1525276 SRX3320765 SRS2626338 SRA623333 GEO Max Delbrück Center 2 0.00264 0.95153 0.00046 0.05429 0.99669 0.88958 0.57635 0.67876 26 100 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44004 44004 SRR6211488 SRX3320763 SRS2626336 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 1 mRNA GSM2830058   source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult Pancreas 1 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Pancreas and liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult GSM2830058 GSM2830058: Pancreas 1 mRNA; Danio rerio; RNA Seq GSM2830058   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830058 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     P5_wt_R1.fastq.gz P5_wt_R2.fastq.gz fastq fastq 18116725914.0 143783539.0 GSM2830058 r1 0:26 1:100 A:5348935548;C:3950936592;G:4404689151;T:4409667387;N:2497236 26 100     5348935548 3950936592 4404689151 4409667387 2497236 SRX3320763 SRS2626336 SRA623333 GEO Max Delbrück Center 2 0.00319 0.93498 0.00092 0.08656 0.9947 0.86097 0.45652 0.53817 26 100 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44008 44008 SRR6211484 SRX3320759 SRS2626332 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 2 scar GSM2830055   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 2 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM2830055 GSM2830055: Heart 2 scar; Danio rerio; OTHER GSM2830055   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830055 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     H6_scar_R1.fastq.gz H6_scar_R2.fastq.gz fastq fastq 2079107172.0 15065994.0 GSM2830055 r1 0:28 1:110 A:580640871;C:641740953;G:501505035;T:355092832;N:127481 28 110     580640871 641740953 501505035 355092832 127481 SRX3320759 SRS2626332 SRA623333 GEO Max Delbrück Center 2 5e-05 0.00253 4e-05 0.00023 1.0 0.99778   0.58419 28 110 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44009 44009 SRR6211483 SRX3320758 SRS2626348 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 2 scar GSM2830054   source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult Pancreas 2 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Pancreas and liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult GSM2830054 GSM2830054: Pancreas 2 scar; Danio rerio; OTHER GSM2830054   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830054 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     P6_scar_R1.fastq.gz P6_scar_R2.fastq.gz fastq fastq 1026715860.0 7439970.0 GSM2830054 r1 0:28 1:110 A:287816843;C:320879355;G:243598630;T:174359452;N:61580 28 110     287816843 320879355 243598630 174359452 61580 SRX3320758 SRS2626348 SRA623333 GEO Max Delbrück Center 2 0.00029 0.00123 0.00028 6e-05 1.0 0.99914   0.25714 28 110 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44010 44010 SRR6211482 SRX3320757 SRS2626331 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Heart 1 scar GSM2830053   source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult Heart 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Heart and blood   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult GSM2830053 GSM2830053: Heart 1 scar; Danio rerio; OTHER GSM2830053   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830053 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     H5_scar_R1.fastq.gz H5_scar_R2.fastq.gz fastq fastq 1287546624.0 10218624.0 GSM2830053 r1 0:26 1:100 A:365272675;C:413037677;G:296495693;T:212570153;N:170426 26 100     365272675 413037677 296495693 212570153 170426 SRX3320757 SRS2626331 SRA623333 GEO Max Delbrück Center 2 0.00023 0.00044 0.00022 3e-05 1.0 0.99955   0.32653 26 100 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
44012 44012 SRR6211480 SRX3320755 SRS2626329 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 1 scar GSM2830051   source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult Pancreas 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Pancreas and liver   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult GSM2830051 GSM2830051: Pancreas 1 scar; Danio rerio; OTHER GSM2830051   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830051 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     P5_scar_R1.fastq.gz P5_scar_R2.fastq.gz fastq fastq 1192602600.0 9465100.0 GSM2830051 r1 0:26 1:100 A:346841760;C:383266222;G:268916933;T:193424756;N:152929 26 100     346841760 383266222 268916933 193424756 152929 SRX3320755 SRS2626329 SRA623333 GEO Max Delbrück Center 2 0.00021 0.00091 0.00014 2e-05 0.99997 0.99892 0.0 0.23931 26 100 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Adult Adult Multi-tissue Multi-system
53493 53493 SRR9881612 SRX6634133 SRS5205093 SRP217216 PRJNA558070 N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells GSE135246 Transcriptome Analysis Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds   pubmed:33273096   223mut 27hpf EC1 GSM3996907   source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut 223mut 27hpf EC1 The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition. endothelial cell   Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1 Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473. tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut GSM3996907 GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq GSM3996907   1 Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1 GEO Accession:GSM3996907 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217216     Mut_pssorted_genome_bam.bam 10X Genomics bam file 31174899854.0 318111223.0 GSM3996907 r1 0:98 A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422 98       8464403532 7291172763 7282393533 8131647604 5282422 SRX6634133 SRS5205093 SRA930499 GEO Internal Medicine, Yale University 1 0.92745   0.05306   0.84502   0.46383   98   B   usable mapping rate illumina hiseq_era unknown small_rna unknown sc single_cell_droplet 10x   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
53494 53494 SRR9881611 SRX6634132 SRS5205092 SRP217216 PRJNA558070 N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells GSE135246 Transcriptome Analysis Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds   pubmed:33273096   wildtype 27hpf EC1 GSM3996906   source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype wildtype 27hpf EC1 The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition. endothelial cell   Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1 Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473. tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype GSM3996906 GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq GSM3996906   1 Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1 GEO Accession:GSM3996906 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217216     WT_pssorted_genome_bam.bam 10X Genomics bam file 26866951370.0 274152565.0 GSM3996906 r1 0:98 A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360 98       7373453026 6169004304 6196779570 7121490110 6224360 SRX6634132 SRS5205092 SRA930499 GEO Internal Medicine, Yale University 1 0.93015   0.0602   0.83853   0.4683   98   B   usable mapping rate illumina hiseq_era unknown small_rna unknown sc single_cell_droplet 10x   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
56706 56706 SRR11040640 SRX7692417 SRS6118510 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3lof/lof GSM4301251   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 2 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301251 GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301251   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3lof-R3-ZF-0519_S3_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S3_L001_R2_001.fastq.gz fastq fastq 2956636039.0 24845681.0 GSM4301251 r1 0:28 1:91 A:805752236;C:683372886;G:699894274;T:767405768;N:210875 28 91     805752236 683372886 699894274 767405768 210875 SRX7692417 SRS6118510 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00944 0.95293 0.0032 0.11845 0.98863 0.79573 0.31275 0.48226 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56707 56707 SRR11040641 SRX7692417 SRS6118510 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3lof/lof GSM4301251   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 2 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301251 GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301251   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3lof-R3-ZF-0519_S4_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S4_L001_R2_001.fastq.gz fastq fastq 2943149888.0 24732352.0 GSM4301251 r2 0:28 1:91 A:801299410;C:680335967;G:696876648;T:764428085;N:209778 28 91     801299410 680335967 696876648 764428085 209778 SRX7692417 SRS6118510 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00982 0.95341 0.00295 0.11853 0.98798 0.79429 0.32383 0.48491 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56708 56708 SRR11040642 SRX7692417 SRS6118510 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3lof/lof GSM4301251   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 2 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301251 GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301251   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3lof-R3-ZF-0519_S8_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S8_L001_R2_001.fastq.gz fastq fastq 2930322283.0 24624557.0 GSM4301251 r3 0:28 1:91 A:800017449;C:676370110;G:692286275;T:761438555;N:209894 28 91     800017449 676370110 692286275 761438555 209894 SRX7692417 SRS6118510 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.0091 0.95344 0.00277 0.11835 0.98863 0.79523 0.30888 0.47399 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56709 56709 SRR11040643 SRX7692417 SRS6118510 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3lof/lof GSM4301251   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 2 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301251 GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301251   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3lof-R3-ZF-0519_S10_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S10_L001_R2_001.fastq.gz fastq fastq 3086393758.0 25936082.0 GSM4301251 r4 0:28 1:91 A:842498816;C:712567363;G:729291108;T:801817022;N:219449 28 91     842498816 712567363 729291108 801817022 219449 SRX7692417 SRS6118510 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00907 0.95227 0.00303 0.11898 0.98906 0.79555 0.32194 0.48998 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56710 56710 SRR11040636 SRX7692416 SRS6118508 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3lof/lof GSM4301250   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 1 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301250 GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301250   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3lof-R3-ZF-0519_S2_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S2_L001_R2_001.fastq.gz fastq fastq 3809919113.0 32016127.0 GSM4301250 r1 0:28 1:91 A:1051323356;C:870053361;G:886403932;T:1001865374;N:273090 28 91     1051323356 870053361 886403932 1001865374 273090 SRX7692416 SRS6118508 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.0073 0.95159 0.00239 0.13839 0.98979 0.78293 0.32315 0.49047 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56711 56711 SRR11040637 SRX7692416 SRS6118508 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3lof/lof GSM4301250   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 1 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301250 GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301250   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3lof-R3-ZF-0519_S5_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S5_L001_R2_001.fastq.gz fastq fastq 5231239643.0 43959997.0 GSM4301250 r2 0:28 1:91 A:1444902743;C:1193884261;G:1216010955;T:1376068197;N:373487 28 91     1444902743 1193884261 1216010955 1376068197 373487 SRX7692416 SRS6118508 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00703 0.95125 0.00257 0.13933 0.99062 0.78417 0.33564 0.4777 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56712 56712 SRR11040638 SRX7692416 SRS6118508 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3lof/lof GSM4301250   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 1 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301250 GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301250   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3lof-R3-ZF-0519_S14_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S14_L001_R2_001.fastq.gz fastq fastq 6034697060.0 50711740.0 GSM4301250 r3 0:28 1:91 A:1667295741;C:1376061258;G:1401956669;T:1588951873;N:431519 28 91     1667295741 1376061258 1401956669 1588951873 431519 SRX7692416 SRS6118508 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00707 0.94822 0.00239 0.13943 0.99038 0.78311 0.36655 0.47115 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56713 56713 SRR11040639 SRX7692416 SRS6118508 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3lof/lof GSM4301250   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm 1 fgfr3lof/lof Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm GSM4301250 GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq GSM4301250   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3lof-R3-ZF-0519_S15_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S15_L001_R2_001.fastq.gz fastq fastq 5425038164.0 45588556.0 GSM4301250 r4 0:28 1:91 A:1498130539;C:1238395410;G:1261876829;T:1426249730;N:385656 28 91     1498130539 1238395410 1261876829 1426249730 385656 SRX7692416 SRS6118508 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00733 0.94973 0.0026 0.13793 0.99068 0.78423 0.3337 0.48233 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56714 56714 SRR11040632 SRX7692415 SRS6118509 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3+/+ GSM4301249   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 2 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301249 GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq GSM4301249   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3plus-R3-ZF-0519_S6_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S6_L001_R2_001.fastq.gz fastq fastq 4962416501.0 41700979.0 GSM4301249 r1 0:28 1:91 A:1356709063;C:1139750321;G:1170875983;T:1294727572;N:353562 28 91     1356709063 1139750321 1170875983 1294727572 353562 SRX7692415 SRS6118509 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00727 0.95235 0.00248 0.13046 0.98981 0.78054 0.33659 0.48621 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56715 56715 SRR11040633 SRX7692415 SRS6118509 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3+/+ GSM4301249   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 2 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301249 GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq GSM4301249   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3plus-R3-ZF-0519_S12_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S12_L001_R2_001.fastq.gz fastq fastq 6695697316.0 56266364.0 GSM4301249 r2 0:28 1:91 A:1829441811;C:1538021924;G:1580312219;T:1747444971;N:476391 28 91     1829441811 1538021924 1580312219 1747444971 476391 SRX7692415 SRS6118509 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00744 0.95393 0.0026 0.13086 0.98969 0.78139 0.34081 0.50162 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56716 56716 SRR11040634 SRX7692415 SRS6118509 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3+/+ GSM4301249   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 2 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301249 GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq GSM4301249   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3plus-R3-ZF-0519_S13_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S13_L001_R2_001.fastq.gz fastq fastq 4853594809.0 40786511.0 GSM4301249 r3 0:28 1:91 A:1328029955;C:1113808349;G:1144735618;T:1266673333;N:347554 28 91     1328029955 1113808349 1144735618 1266673333 347554 SRX7692415 SRS6118509 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00737 0.95245 0.00274 0.12891 0.99038 0.78228 0.3487 0.4977 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56717 56717 SRR11040635 SRX7692415 SRS6118509 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   2 fgfr3+/+ GSM4301249   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 2 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301249 GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq GSM4301249   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     2-fgfr3plus-R3-ZF-0519_S16_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S16_L001_R2_001.fastq.gz fastq fastq 6323597406.0 53139474.0 GSM4301249 r4 0:28 1:91 A:1727515649;C:1453521438;G:1493844843;T:1648265752;N:449724 28 91     1727515649 1453521438 1493844843 1648265752 449724 SRX7692415 SRS6118509 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00737 0.95341 0.00266 0.12818 0.98934 0.78151 0.32417 0.4918 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56718 56718 SRR11040628 SRX7692414 SRS6118507 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3+/+ GSM4301248   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 1 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301248 GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq GSM4301248   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3plus-R3-ZF-0519_S1_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S1_L001_R2_001.fastq.gz fastq fastq 6286029939.0 52823781.0 GSM4301248 r1 0:28 1:91 A:1726222024;C:1448493933;G:1483478967;T:1627385939;N:449076 28 91     1726222024 1448493933 1483478967 1627385939 449076 SRX7692414 SRS6118507 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00651 0.95215 0.0021 0.11197 0.99099 0.79914 0.32593 0.49237 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56719 56719 SRR11040629 SRX7692414 SRS6118507 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3+/+ GSM4301248   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 1 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301248 GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq GSM4301248   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3plus-R3-ZF-0519_S7_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S7_L001_R2_001.fastq.gz fastq fastq 5384386336.0 45246944.0 GSM4301248 r2 0:28 1:91 A:1482057664;C:1241359922;G:1266945881;T:1393638700;N:384169 28 91     1482057664 1241359922 1266945881 1393638700 384169 SRX7692414 SRS6118507 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00644 0.9527 0.00205 0.11156 0.99111 0.80217 0.3568 0.48853 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56720 56720 SRR11040630 SRX7692414 SRS6118507 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3+/+ GSM4301248   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 1 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301248 GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq GSM4301248   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3plus-R3-ZF-0519_S9_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S9_L001_R2_001.fastq.gz fastq fastq 5916050133.0 49714707.0 GSM4301248 r3 0:28 1:91 A:1628484212;C:1362413135;G:1391038139;T:1533691145;N:423502 28 91     1628484212 1362413135 1391038139 1533691145 423502 SRX7692414 SRS6118507 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.0066 0.95312 0.00209 0.11367 0.99109 0.79857 0.336 0.47399 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
56721 56721 SRR11040631 SRX7692414 SRS6118507 SRP247644 PRJNA605419 FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development GSE144944 Transcriptome Analysis In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   pubmed:32379366   1 fgfr3+/+ GSM4301248   source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm 1 fgfr3+/+ Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx Cranial vault   The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.   tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm GSM4301248 GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq GSM4301248   1 The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell. GEO Accession:GSM4301248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP247644     1-fgfr3plus-R3-ZF-0519_S11_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S11_L001_R2_001.fastq.gz fastq fastq 5591429319.0 46986801.0 GSM4301248 r4 0:28 1:91 A:1539075154;C:1286758672;G:1316467634;T:1448729317;N:398542 28 91     1539075154 1286758672 1316467634 1448729317 398542 SRX7692414 SRS6118507 SRA1039424 GEO Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine 2 0.00664 0.95136 0.00216 0.11396 0.99131 0.8003 0.32678 0.49629 28 91 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified trueseq sc single_cell_droplet 10x   France 2020-02-07 Undetermined Undetermined Multi-tissue Multi-system
59196 59196 SRR11777188 SRX8330063 SRS6649550 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 3 GSM4547702   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 3 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547702 GSM4547702: dominant 3; Danio rerio; RNA Seq GSM4547702   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547702 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample8 I1.fastq.gz read2PairFiles=Next sample8 R1.fastq.gz read3PairFiles=Next sample8 R2.fastq.gz Next_sample8_I1.fastq.gz Next_sample8_R1.fastq.gz Next_sample8_R2.fastq.gz fastq fastq fastq 6949629860.0 75539455.0 GSM4547702 r1 0:8 1:26 2:58 A:1844979631;C:1603125876;G:1713257721;T:1782703901;N:5562731 8 26 58   1844979631 1603125876 1713257721 1782703901 5562731 SRX8330063 SRS6649550 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95614   0.07196   0.85527   0.53876   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59197 59197 SRR11777189 SRX8330063 SRS6649550 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 3 GSM4547702   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 3 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547702 GSM4547702: dominant 3; Danio rerio; RNA Seq GSM4547702   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547702 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample8 S8 L001 I1 001.fastq.gz read2PairFiles=sample8 S8 L001 R1 001.fastq.gz read3PairFiles=sample8 S8 L001 R2 001.fastq.gz sample8_S8_L001_R2_001.fastq.gz sample8_S8_L001_R1_001.fastq.gz sample8_S8_L001_I1_001.fastq.gz fastq fastq fastq 37968081102.0 301333977.0 GSM4547702 r2 0:8 1:26 2:92 A:10580168599;C:8638562811;G:9024245345;T:9723132070;N:1972277 8 26 92   10580168599 8638562811 9024245345 9723132070 1972277 SRX8330063 SRS6649550 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95282   0.06548   0.8546   0.52648   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59198 59198 SRR11777190 SRX8330063 SRS6649550 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 3 GSM4547702   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 3 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547702 GSM4547702: dominant 3; Danio rerio; RNA Seq GSM4547702   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547702 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample8 S8 L002 I1 001.fastq.gz read2PairFiles=sample8 S8 L002 R1 001.fastq.gz read3PairFiles=sample8 S8 L002 R2 001.fastq.gz sample8_S8_L002_R2_001.fastq.gz sample8_S8_L002_R1_001.fastq.gz sample8_S8_L002_I1_001.fastq.gz fastq fastq fastq 37640109906.0 298731031.0 GSM4547702 r3 0:8 1:26 2:92 A:10490817242;C:8564221041;G:8946179351;T:9637119181;N:1773091 8 26 92   10490817242 8564221041 8946179351 9637119181 1773091 SRX8330063 SRS6649550 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95231   0.06664   0.85326   0.52977   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59199 59199 SRR11777185 SRX8330062 SRS6649549 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 2 GSM4547701   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 2 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547701 GSM4547701: dominant 2; Danio rerio; RNA Seq GSM4547701   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547701 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample7 I1.fastq.gz read2PairFiles=Next sample7 R1.fastq.gz read3PairFiles=Next sample7 R2.fastq.gz Next_sample7_R2.fastq.gz Next_sample7_R1.fastq.gz Next_sample7_I1.fastq.gz fastq fastq fastq 8529279244.0 92709557.0 GSM4547701 r1 0:8 1:26 2:58 A:2302811456;C:1921371420;G:2078302909;T:2219976032;N:6817427 8 26 58   2302811456 1921371420 2078302909 2219976032 6817427 SRX8330062 SRS6649549 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.94004   0.09046   0.85555   0.50147   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59200 59200 SRR11777186 SRX8330062 SRS6649549 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 2 GSM4547701   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 2 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547701 GSM4547701: dominant 2; Danio rerio; RNA Seq GSM4547701   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547701 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample7 S7 L001 I1 001.fastq.gz read2PairFiles=sample7 S7 L001 R1 001.fastq.gz read3PairFiles=sample7 S7 L001 R2 001.fastq.gz sample7_S7_L001_R2_001.fastq.gz sample7_S7_L001_R1_001.fastq.gz sample7_S7_L001_I1_001.fastq.gz fastq fastq fastq 34725493026.0 275599151.0 GSM4547701 r2 0:8 1:26 2:92 A:9769026986;C:7706289537;G:8194381066;T:9053981896;N:1813541 8 26 92   9769026986 7706289537 8194381066 9053981896 1813541 SRX8330062 SRS6649549 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.9448   0.0817   0.85336   0.52553   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59201 59201 SRR11777187 SRX8330062 SRS6649549 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 2 GSM4547701   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 2 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547701 GSM4547701: dominant 2; Danio rerio; RNA Seq GSM4547701   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547701 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample7 S7 L002 I1 001.fastq.gz read2PairFiles=sample7 S7 L002 R1 001.fastq.gz read3PairFiles=sample7 S7 L002 R2 001.fastq.gz sample7_S7_L002_R2_001.fastq.gz sample7_S7_L002_R1_001.fastq.gz sample7_S7_L002_I1_001.fastq.gz fastq fastq fastq 34468767648.0 273561648.0 GSM4547701 r3 0:8 1:26 2:92 A:9700179724;C:7649330815;G:8132966012;T:8984661489;N:1629608 8 26 92   9700179724 7649330815 8132966012 8984661489 1629608 SRX8330062 SRS6649549 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.94359   0.08201   0.85206   0.52394   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59202 59202 SRR11777182 SRX8330061 SRS6649548 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 1 GSM4547700   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 1 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547700 GSM4547700: dominant 1; Danio rerio; RNA Seq GSM4547700   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547700 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample6 I1.fastq.gz read2PairFiles=Next sample6 R1.fastq.gz read3PairFiles=Next sample6 R2.fastq.gz Next_sample6_R2.fastq.gz Next_sample6_R1.fastq.gz Next_sample6_I1.fastq.gz fastq fastq fastq 7186504192.0 78114176.0 GSM4547700 r1 0:8 1:26 2:58 A:1890231359;C:1687648873;G:1767027837;T:1835889658;N:5706465 8 26 58   1890231359 1687648873 1767027837 1835889658 5706465 SRX8330061 SRS6649548 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95103   0.08633   0.84997   0.5111   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59203 59203 SRR11777183 SRX8330061 SRS6649548 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 1 GSM4547700   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 1 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547700 GSM4547700: dominant 1; Danio rerio; RNA Seq GSM4547700   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547700 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample6 S6 L001 I1 001.fastq.gz read2PairFiles=sample6 S6 L001 R1 001.fastq.gz read3PairFiles=sample6 S6 L001 R2 001.fastq.gz sample6_S6_L001_R2_001.fastq.gz sample6_S6_L001_R1_001.fastq.gz sample6_S6_L001_I1_001.fastq.gz fastq fastq fastq 35787988152.0 284031652.0 GSM4547700 r2 0:8 1:26 2:92 A:9781991861;C:8320736351;G:8552750572;T:9130655372;N:1853996 8 26 92   9781991861 8320736351 8552750572 9130655372 1853996 SRX8330061 SRS6649548 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95998   0.0809   0.84891   0.53314   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59204 59204 SRR11777184 SRX8330061 SRS6649548 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   dominant 1 GSM4547700   tissue:dominant|cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color dominant 1 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms dominant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:sorted single color kidney marrow cells|sorting:sorted|age:8 mpf|genotype/variation:dominant Zebrabow color GSM4547700 GSM4547700: dominant 1; Danio rerio; RNA Seq GSM4547700   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547700 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample6 S6 L002 I1 001.fastq.gz read2PairFiles=sample6 S6 L002 R1 001.fastq.gz read3PairFiles=sample6 S6 L002 R2 001.fastq.gz sample6_S6_L002_R2_001.fastq.gz sample6_S6_L002_R1_001.fastq.gz sample6_S6_L002_I1_001.fastq.gz fastq fastq fastq 35545836942.0 282109817.0 GSM4547700 r3 0:8 1:26 2:92 A:9719207479;C:8264195207;G:8494199037;T:9066565654;N:1669565 8 26 92   9719207479 8264195207 8494199037 9066565654 1669565 SRX8330061 SRS6649548 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95974   0.0796   0.85036   0.54185   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59205 59205 SRR11777179 SRX8330060 SRS6649547 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   mutant 3 GSM4547699   tissue:mutant|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 mpf|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA mutant 3 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms mutant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 mpf|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA GSM4547699 GSM4547699: mutant 3; Danio rerio; RNA Seq GSM4547699   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547699 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample5 I1.fastq.gz read2PairFiles=Next sample5 R1.fastq.gz read3PairFiles=Next sample5 R2.fastq.gz Next_sample5_R2.fastq.gz Next_sample5_R1.fastq.gz Next_sample5_I1.fastq.gz fastq fastq fastq 7160703436.0 77833733.0 GSM4547699 r1 0:8 1:26 2:58 A:1816363574;C:1765855914;G:1734024608;T:1838721304;N:5738036 8 26 58   1816363574 1765855914 1734024608 1838721304 5738036 SRX8330060 SRS6649547 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.95273   0.06131   0.85693   0.50453   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system
59206 59206 SRR11777180 SRX8330060 SRS6649547 SRP261272 PRJNA631927 Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I] GSE150373 Transcriptome Analysis Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish. parent bioproject:PRJNA734615 pubmed:34735227   mutant 3 GSM4547699   tissue:mutant|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 mpf|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA mutant 3 The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms mutant No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 mpf|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA GSM4547699 GSM4547699: mutant 3; Danio rerio; RNA Seq GSM4547699   1 post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics GEO Accession:GSM4547699 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP261272   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=sample5 S5 L001 I1 001.fastq.gz read2PairFiles=sample5 S5 L001 R1 001.fastq.gz read3PairFiles=sample5 S5 L001 R2 001.fastq.gz sample5_S5_L001_R2_001.fastq.gz sample5_S5_L001_R1_001.fastq.gz sample5_S5_L001_I1_001.fastq.gz fastq fastq fastq 39409717914.0 312775539.0 GSM4547699 r2 0:8 1:26 2:92 A:10331447053;C:9658224477;G:9315034438;T:10102971653;N:2040293 8 26 92   10331447053 9658224477 9315034438 10102971653 2040293 SRX8330060 SRS6649547 SRA1074695 GEO Oncology/Hematology, Boston Children's Hospital 1 0.96833   0.05626   0.85336   0.50422   92   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-05-12 Adult Adult Multi-tissue Multi-system

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;