rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
10163,ERR5714657,ERX5430029,ERS6251768,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,WT,SAMEA8567093,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567093|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:WT|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:head kidney|sample name:E MTAB 10360:WT|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:WT p,WT p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,WT.bam,bam,1041394032.0,18596322.0,E MTAB 10360:WT,0:56,A:284652376;C:244349479;G:255850754;T:255536179;N:1005244,56,,,,284652376,244349479,255850754,255536179,1005244,ERX5430029,ERS6251768,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.9192,,0.10547,,0.84782,,0.53778,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10164,ERR5714656,ERX5430028,ERS6251767,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Rb,SAMEA8567092,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567092|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Rb|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1rb4bp|organism part:head kidney|sample name:E MTAB 10360:Rb|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Rb p,Rb p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1rb4bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Rb.bam,bam,1069920824.0,19105729.0,E MTAB 10360:Rb,0:56,A:299856824;C:238947539;G:256649537;T:273433744;N:1033180,56,,,,299856824,238947539,256649537,273433744,1033180,ERX5430028,ERS6251767,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.94145,,0.11133,,0.83191,,0.52892,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10165,ERR5714655,ERX5430027,ERS6251766,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Ra,SAMEA8567091,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567091|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Ra|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1ra5bp|organism part:head kidney|sample name:E MTAB 10360:Ra|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Ra p,Ra p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1ra5bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Ra.bam,bam,1009240400.0,18022150.0,E MTAB 10360:Ra,0:56,A:279849736;C:230130588;G:247312130;T:250994600;N:953346,56,,,,279849736,230130588,247312130,250994600,953346,ERX5430027,ERS6251766,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.95705,,0.10915,,0.84788,,0.47011,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 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,,,,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,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 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,,,,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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
66749,SRR23717086,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L001_R1_001.fastq.gz 210954C_spi2_MO_S1_L001_R2_001.fastq.gz,fastq fastq,38657555700.0,128858519.0,GSM7083029 r1,0:150 1:150,A:16254027461;C:6972577611;G:6733828903;T:8696771854;N:349871,150,150,,,16254027461,6972577611,6733828903,8696771854,349871,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92157,0.0,0.12849,1.0,0.7811,,0.5613,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66750,SRR23717087,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L002_R1_001.fastq.gz 210954C_spi2_MO_S1_L002_R2_001.fastq.gz,fastq fastq,39767723700.0,132559079.0,GSM7083029 r2,0:150 1:150,A:16740739613;C:7166687108;G:6926997738;T:8932937589;N:361652,150,150,,,16740739613,7166687108,6926997738,8932937589,361652,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92006,0.0,0.12624,1.0,0.7808,,0.56645,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66751,SRR23717088,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L003_R1_001.fastq.gz 210954C_spi2_MO_S1_L003_R2_001.fastq.gz,fastq fastq,33826342500.0,112754475.0,GSM7083029 r3,0:150 1:150,A:14247560719;C:6101219095;G:5882384356;T:7594866748;N:311582,150,150,,,14247560719,6101219095,5882384356,7594866748,311582,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91535,0.0,0.12519,1.0,0.7833,,0.56425,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66752,SRR23717089,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L004_R1_001.fastq.gz 210954C_spi2_MO_S1_L004_R2_001.fastq.gz,fastq fastq,42436674900.0,141455583.0,GSM7083029 r4,0:150 1:150,A:17850346993;C:7641162936;G:7380219938;T:9564565232;N:379801,150,150,,,17850346993,7641162936,7380219938,9564565232,379801,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91972,0.0,0.12638,1.0,0.78131,,0.56385,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66753,SRR16539848,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_1_1_R1.fq.gz 190718O_ECHEHSC_R_1_1_R2.fq.gz,fastq fastq,42862683000.0,142875610.0,GSM5651458 r1,0:150 1:150,A:19056076938;C:7513613524;G:7148399243;T:9144249423;N:343872,150,150,,,19056076938,7513613524,7148399243,9144249423,343872,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92848,0.0,0.09872,1.0,0.81797,,0.52595,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66754,SRR16539849,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_2_1_R1.fq.gz 190718O_ECHEHSC_R_2_1_R2.fq.gz,fastq fastq,45613780500.0,152045935.0,GSM5651458 r2,0:150 1:150,A:20279847027;C:7989810705;G:7602659881;T:9741099780;N:363107,150,150,,,20279847027,7989810705,7602659881,9741099780,363107,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92821,0.0,0.09747,1.0,0.81706,,0.52451,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66755,SRR16539850,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_3_1_R1.fq.gz 190718O_ECHEHSC_R_3_1_R2.fq.gz,fastq fastq,57137293500.0,190457645.0,GSM5651458 r3,0:150 1:150,A:25401821096;C:10031650741;G:9533037288;T:12170324099;N:460276,150,150,,,25401821096,10031650741,9533037288,12170324099,460276,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92958,0.0,0.09774,1.0,0.81773,,0.52455,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66756,SRR16539851,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_4_1_R1.fq.gz 190718O_ECHEHSC_R_4_1_R2.fq.gz,fastq fastq,29835023100.0,99450077.0,GSM5651458 r4,0:150 1:150,A:13290644326;C:5233486555;G:4966979633;T:6343677510;N:235076,150,150,,,13290644326,5233486555,4966979633,6343677510,235076,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92872,0.0,0.098,1.0,0.8185,,0.52198,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
71058,SRR21152616,SRX17164237,SRS14735586,SRP393251,PRJNA871903,Single cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes,GSE211728,Transcriptome Analysis,A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non mammalian vertebrates such as zebrafish  regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability  the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non sensory supporting cells. We identify a putative progenitor population for hair and supporting cells  as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line  a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae  we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs  the utricle and saccule  consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear specific hair cell function and regeneration. Overall design: Inner ears were dissected from the Sox10Cre;UbiSwitch zebrafish at 14dpf n=35 and 12mpf n=6. Converted cells were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of mCherry signal and analyzed using 10x genomics based scRNAseq. Reads were aligned to danRer11 using the Cellranger pipeline,,pubmed:36598134,,12mpf Sox10CreUbiswitch ear,GSM6500164,,source name:inner ear|tissue:inner ear|sample type:nuclear RNA|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:12 mpf,12mpf Sox10CreUbiswitch ear,Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 14dpf or cellranger arc count v2.0.0 12mpf Downstream analysis was performed in R and Python Assembly: danRer11 Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries  including the two libraries here and other published data,inner ear,,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,tissue:inner ear|sample type:nuclear RNA|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:12 mpf,GSM6500164,GSM6500164: 12mpf Sox10CreUbiswitch ear; Danio rerio; RNA Seq,GSM6500164 r1,GSM6500164,1,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer's solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP393251,,loader:fastq load.py,sox10Cre_UbiSwitch_12mpf_ear_snRNA1_S6_L001_R1_001.fastq.gz sox10Cre_UbiSwitch_12mpf_ear_snRNA1_S6_L001_R2_001.fastq.gz,fastq fastq,16297154772.0,123961990.0,GSM6500164 r1,0:29 1:102.47,A:4776377223;C:3475545962;G:3470510289;T:4559999591;N:14721707,29,102,,,4776377223,3475545962,3470510289,4559999591,14721707,SRX17164237,SRS14735586,SRA1480233,University of Southern California,University of Southern California,2,0.0107,0.86542,0.00542,0.28105,0.99208,0.83329,0.49663,0.78501,29,102,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-21,Adult,Adult,Multi-tissue,Multi-system
71059,SRR21152617,SRX17164236,SRS14735585,SRP393251,PRJNA871903,Single cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes,GSE211728,Transcriptome Analysis,A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non mammalian vertebrates such as zebrafish  regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability  the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non sensory supporting cells. We identify a putative progenitor population for hair and supporting cells  as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line  a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae  we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs  the utricle and saccule  consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear specific hair cell function and regeneration. Overall design: Inner ears were dissected from the Sox10Cre;UbiSwitch zebrafish at 14dpf n=35 and 12mpf n=6. Converted cells were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of mCherry signal and analyzed using 10x genomics based scRNAseq. Reads were aligned to danRer11 using the Cellranger pipeline,,pubmed:36598134,,14dpf Sox10CreUbiswitch ear,GSM6500163,,source name:inner ear|tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf,14dpf Sox10CreUbiswitch ear,Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 14dpf or cellranger arc count v2.0.0 12mpf Downstream analysis was performed in R and Python Assembly: danRer11 Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries  including the two libraries here and other published data,inner ear,,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf,GSM6500163,GSM6500163: 14dpf Sox10CreUbiswitch ear; Danio rerio; RNA Seq,GSM6500163 r1,GSM6500163,1,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer's solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP393251,,loader:fastq load.py,sox10CreUbiSwitch_14dpf_ear_S1_L001_R1_001.fastq.gz sox10CreUbiSwitch_14dpf_ear_S1_L001_R2_001.fastq.gz,fastq fastq,66312808744.0,512252644.0,GSM6500163 r1,0:29 1:100.45,A:19003048692;C:14320898403;G:14949837823;T:17995908285;N:43115541,29,100,,,19003048692,14320898403,14949837823,17995908285,43115541,SRX17164236,SRS14735585,SRA1480233,University of Southern California,University of Southern California,2,0.0023,0.91017,0.00102,0.17968,0.99642,0.78338,0.36213,0.5439,29,101,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-21,Larval,Larval,Multi-tissue,Multi-system
72189,SRR22306352,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_A_S2_L001_I1_001.fastq.gz 144hpf_A_S2_L001_R1_001.fastq.gz 144hpf_A_S2_L001_R2_001.fastq.gz,fastq fastq fastq,10071479082.0,54147737.0,GSM6734161 r1,0:8 1:28 2:150,A:2929773310;C:1499798320;G:1653059165;T:2039362600;N:167155,8,28,150,,2929773310,1499798320,1653059165,2039362600,167155,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.74663,,0.09604,,0.81475,,0.47201,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72190,SRR22306353,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_A_S2_L002_I1_001.fastq.gz 144hpf_A_S2_L002_R1_001.fastq.gz 144hpf_A_S2_L002_R2_001.fastq.gz,fastq fastq fastq,10051484826.0,54040241.0,GSM6734161 r2,0:8 1:28 2:150,A:2923933238;C:1496361942;G:1650442691;T:2035100583;N:197696,8,28,150,,2923933238,1496361942,1650442691,2035100583,197696,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.7469,,0.09438,,0.81168,,0.47634,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72191,SRR22306354,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_B_S4_L001_I1_001.fastq.gz 144hpf_B_S4_L001_R1_001.fastq.gz 144hpf_B_S4_L001_R2_001.fastq.gz,fastq fastq fastq,11611117518.0,62425363.0,GSM6734161 r3,0:8 1:28 2:150,A:2750439378;C:2074542937;G:2235087515;T:2303545516;N:189104,8,28,150,,2750439378,2074542937,2235087515,2303545516,189104,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92993,,0.07791,,0.83057,,0.56478,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72192,SRR22306355,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_B_S4_L002_I1_001.fastq.gz 144hpf_B_S4_L002_R1_001.fastq.gz 144hpf_B_S4_L002_R2_001.fastq.gz,fastq fastq fastq,11608408986.0,62410801.0,GSM6734161 r4,0:8 1:28 2:150,A:2749171529;C:2074699135;G:2234953447;T:2302569589;N:226450,8,28,150,,2749171529,2074699135,2234953447,2302569589,226450,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.93005,,0.07789,,0.83067,,0.56996,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72193,SRR22306356,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_A_S4_L001_I1_001.fastq.gz 120hpf_A_S4_L001_R1_001.fastq.gz 120hpf_A_S4_L001_R2_001.fastq.gz,fastq fastq fastq,17661611028.0,94954898.0,GSM6734160 r1,0:8 1:28 2:150,A:3911517668;C:3269703971;G:3622776955;T:3438794975;N:441131,8,28,150,,3911517668,3269703971,3622776955,3438794975,441131,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92039,,0.2409,,0.82227,,0.62515,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72194,SRR22306357,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_A_S4_L002_I1_001.fastq.gz 120hpf_A_S4_L002_R1_001.fastq.gz 120hpf_A_S4_L002_R2_001.fastq.gz,fastq fastq fastq,18210223794.0,97904429.0,GSM6734160 r2,0:8 1:28 2:150,A:4026424182;C:3375187630;G:3741403732;T:3542247007;N:401799,8,28,150,,4026424182,3375187630,3741403732,3542247007,401799,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92102,,0.24243,,0.82026,,0.62741,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72195,SRR22306358,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_B_S1_L001_I1_001.fastq.gz 120hpf_B_S1_L001_R1_001.fastq.gz 120hpf_B_S1_L001_R2_001.fastq.gz,fastq fastq fastq,11209538124.0,60266334.0,GSM6734160 r3,0:8 1:28 2:150,A:2632527168;C:1943667010;G:2109734084;T:2353841888;N:179950,8,28,150,,2632527168,1943667010,2109734084,2353841888,179950,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.93483,,0.10541,,0.77632,,0.50937,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72196,SRR22306359,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_B_S1_L002_I1_001.fastq.gz 120hpf_B_S1_L002_R1_001.fastq.gz 120hpf_B_S1_L002_R2_001.fastq.gz,fastq fastq fastq,11215815810.0,60300085.0,GSM6734160 r4,0:8 1:28 2:150,A:2633236795;C:1945196823;G:2111252224;T:2355107347;N:219561,8,28,150,,2633236795,1945196823,2111252224,2355107347,219561,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.9355,,0.10564,,0.77798,,0.51829,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72197,SRR22306360,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_A_S2_L001_I1_001.fastq.gz 96hpf_A_S2_L001_R1_001.fastq.gz 96hpf_A_S2_L001_R2_001.fastq.gz,fastq fastq fastq,21803548308.0,117223378.0,GSM6734159 r1,0:8 1:28 2:150,A:5482362998;C:3549501923;G:3687762678;T:4863332303;N:546798,8,28,150,,5482362998,3549501923,3687762678,4863332303,546798,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.89515,,0.20559,,0.77676,,0.58787,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72198,SRR22306361,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_A_S2_L002_I1_001.fastq.gz 96hpf_A_S2_L002_R1_001.fastq.gz 96hpf_A_S2_L002_R2_001.fastq.gz,fastq fastq fastq,22445964780.0,120677230.0,GSM6734159 r2,0:8 1:28 2:150,A:5637460026;C:3657615123;G:3802504010;T:5003513398;N:491943,8,28,150,,5637460026,3657615123,3802504010,5003513398,491943,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.89574,,0.20506,,0.77668,,0.57624,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72199,SRR22306362,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_B_S3_L001_I1_001.fastq.gz 96hpf_B_S3_L001_R1_001.fastq.gz 96hpf_B_S3_L001_R2_001.fastq.gz,fastq fastq fastq,19064211546.0,102495761.0,GSM6734159 r3,0:8 1:28 2:150,A:4336439967;C:3483771778;G:3805326765;T:3748351811;N:473829,8,28,150,,4336439967,3483771778,3805326765,3748351811,473829,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.91875,,0.20874,,0.80298,,0.59387,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72200,SRR22306363,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_B_S3_L002_I1_001.fastq.gz 96hpf_B_S3_L002_R1_001.fastq.gz 96hpf_B_S3_L002_R2_001.fastq.gz,fastq fastq fastq,19616344548.0,105464218.0,GSM6734159 r4,0:8 1:28 2:150,A:4455009353;C:3588592225;G:3922172348;T:3853423493;N:435281,8,28,150,,4455009353,3588592225,3922172348,3853423493,435281,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92045,,0.21078,,0.80322,,0.59961,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72201,SRR22306364,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_A_S3_L003_I1_001.fastq.gz 72hpf_A_S3_L003_R1_001.fastq.gz 72hpf_A_S3_L003_R2_001.fastq.gz,fastq fastq fastq,40892227528.0,222240367.0,GSM6734158 r1,0:8 1:26 2:150,A:11396668180;C:6212386813;G:6930219468;T:8795624716;N:1155873,8,26,150,,11396668180,6212386813,6930219468,8795624716,1155873,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.85155,,0.07413,,0.82416,,0.54356,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72202,SRR22306365,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_B_S1_L001_I1_001.fastq.gz 72hpf_B_S1_L001_R1_001.fastq.gz 72hpf_B_S1_L001_R2_001.fastq.gz,fastq fastq fastq,22062511830.0,118615655.0,GSM6734158 r2,0:8 1:28 2:150,A:5458179709;C:3697017239;G:3917347244;T:4719255263;N:548795,8,28,150,,5458179709,3697017239,3917347244,4719255263,548795,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.90794,,0.20159,,0.77638,,0.60922,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72203,SRR22306366,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_B_S1_L002_I1_001.fastq.gz 72hpf_B_S1_L002_R1_001.fastq.gz 72hpf_B_S1_L002_R2_001.fastq.gz,fastq fastq fastq,22834981176.0,122768716.0,GSM6734158 r3,0:8 1:28 2:150,A:5640789338;C:3831330746;G:4062820506;T:4879868419;N:498391,8,28,150,,5640789338,3831330746,4062820506,4879868419,498391,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.90576,,0.20258,,0.77273,,0.60715,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72204,SRR22306367,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_A_S1_L004_I1_001.fastq.gz 48hpf_A_S1_L004_R1_001.fastq.gz 48hpf_A_S1_L004_R2_001.fastq.gz,fastq fastq fastq,20362974376.0,110668339.0,GSM6734157 r1,0:8 1:26 2:150,A:5123945131;C:3326458224;G:3713701708;T:4435572452;N:573335,8,26,150,,5123945131,3326458224,3713701708,4435572452,573335,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.9134,,0.07314,,0.81379,,0.49083,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
72205,SRR22306368,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_B_S3_L001_I1_001.fastq.gz 48hpf_B_S3_L001_R1_001.fastq.gz 48hpf_B_S3_L001_R2_001.fastq.gz,fastq fastq fastq,12341386626.0,66351541.0,GSM6734157 r2,0:8 1:28 2:150,A:2795275569;C:2297425042;G:2482925319;T:2376906238;N:198982,8,28,150,,2795275569,2297425042,2482925319,2376906238,198982,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.95768,,0.08708,,0.81903,,0.51103,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
72206,SRR22306369,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_B_S3_L002_I1_001.fastq.gz 48hpf_B_S3_L002_R1_001.fastq.gz 48hpf_B_S3_L002_R2_001.fastq.gz,fastq fastq fastq,12292760832.0,66090112.0,GSM6734157 r3,0:8 1:28 2:150,A:2783844388;C:2288795302;G:2473127346;T:2367511149;N:238615,8,28,150,,2783844388,2288795302,2473127346,2367511149,238615,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.95903,,0.08687,,0.82085,,0.53794,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
74464,SRR23824308,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L001_R1_001.fastq.gz Ctrl-WKM-2_S6_L001_R2_001.fastq.gz,fastq fastq,5194270202.0,44019239.0,GSM7092959 r1,0:28 1:90,A:1398515411;C:1233312154;G:1232180674;T:1330142923;N:119040,28,90,,,1398515411,1233312154,1232180674,1330142923,119040,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00309,0.88688,0.0009,0.07597,0.99419,0.8434,0.37081,0.54861,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74465,SRR23824309,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L002_R1_001.fastq.gz Ctrl-WKM-2_S6_L002_R2_001.fastq.gz,fastq fastq,5194814064.0,44023848.0,GSM7092959 r2,0:28 1:90,A:1398346625;C:1233448625;G:1232179725;T:1330726706;N:112383,28,90,,,1398346625,1233448625,1232179725,1330726706,112383,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0031,0.8897,0.00099,0.07765,0.99478,0.84094,0.39012,0.55206,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74466,SRR23824310,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L003_R2_001.fastq.gz Ctrl-WKM-2_S6_L003_R1_001.fastq.gz,fastq fastq,5266248786.0,44629227.0,GSM7092959 r3,0:28 1:90,A:1416990042;C:1250859074;G:1249886002;T:1348408111;N:105557,28,90,,,1416990042,1250859074,1249886002,1348408111,105557,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00326,0.8894,0.00114,0.07686,0.99427,0.84214,0.42716,0.54905,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74467,SRR23824311,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L004_R1_001.fastq.gz Ctrl-WKM-2_S6_L004_R2_001.fastq.gz,fastq fastq,5179146850.0,43891075.0,GSM7092959 r4,0:28 1:90,A:1394750319;C:1229159365;G:1227969525;T:1327168248;N:99393,28,90,,,1394750319,1229159365,1227969525,1327168248,99393,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00344,0.88836,0.00108,0.07651,0.99385,0.84248,0.39035,0.55457,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74468,SRR23824312,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L001_R1_001.fastq.gz Ctrl-WKM-1_S2_L001_R2_001.fastq.gz,fastq fastq,5724434408.0,48512156.0,GSM7092958 r1,0:28 1:90,A:1567228637;C:1329088014;G:1338348271;T:1489638044;N:131442,28,90,,,1567228637,1329088014,1338348271,1489638044,131442,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0034,0.89852,0.00097,0.08358,0.99387,0.82836,0.39872,0.48691,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74469,SRR23824313,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L002_R1_001.fastq.gz Ctrl-WKM-1_S2_L002_R2_001.fastq.gz,fastq fastq,5722747716.0,48497862.0,GSM7092958 r2,0:28 1:90,A:1566186287;C:1328568122;G:1337682111;T:1490187432;N:123764,28,90,,,1566186287,1328568122,1337682111,1490187432,123764,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00351,0.89791,0.00115,0.08308,0.99322,0.82822,0.38209,0.55877,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74470,SRR23824314,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L003_R1_001.fastq.gz Ctrl-WKM-1_S2_L003_R2_001.fastq.gz,fastq fastq,5805211662.0,49196709.0,GSM7092958 r3,0:28 1:90,A:1588459908;C:1348306329;G:1357849856;T:1510477621;N:117948,28,90,,,1588459908,1348306329,1357849856,1510477621,117948,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00339,0.89829,0.00109,0.08199,0.99373,0.82836,0.36629,0.48567,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74471,SRR23824315,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L004_R1_001.fastq.gz Ctrl-WKM-1_S2_L004_R2_001.fastq.gz,fastq fastq,5706596938.0,48360991.0,GSM7092958 r4,0:28 1:90,A:1562421245;C:1324310664;G:1333276899;T:1486479848;N:108282,28,90,,,1562421245,1324310664,1333276899,1486479848,108282,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00325,0.89893,0.001,0.08305,0.99409,0.82771,0.38551,0.48469,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74496,SRR23824340,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L001_R1_001.fastq.gz 7dpi-WKM-2_S22_L001_R2_001.fastq.gz,fastq fastq,5304844816.0,44956312.0,GSM7092951 r1,0:28 1:90,A:1425725106;C:1263648972;G:1258220580;T:1357129924;N:120234,28,90,,,1425725106,1263648972,1258220580,1357129924,120234,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00449,0.86714,0.00129,0.06514,0.99377,0.84303,0.43042,0.57254,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74497,SRR23824341,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L002_R1_001.fastq.gz 7dpi-WKM-2_S22_L002_R2_001.fastq.gz,fastq fastq,5239083180.0,44399010.0,GSM7092951 r2,0:28 1:90,A:1407415782;C:1248027048;G:1242616066;T:1340911648;N:112636,28,90,,,1407415782,1248027048,1242616066,1340911648,112636,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00481,0.86765,0.00132,0.06608,0.99273,0.84187,0.43387,0.56786,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74498,SRR23824354,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L003_R1_001.fastq.gz 7dpi-WKM-2_S22_L003_R2_001.fastq.gz,fastq fastq,5391479826.0,45690507.0,GSM7092951 r3,0:28 1:90,A:1448063662;C:1284822701;G:1279372271;T:1379111804;N:109388,28,90,,,1448063662,1284822701,1279372271,1379111804,109388,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00459,0.86895,0.00137,0.06695,0.99356,0.84488,0.42512,0.57663,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74499,SRR23824355,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L004_R1_001.fastq.gz 7dpi-WKM-2_S22_L004_R2_001.fastq.gz,fastq fastq,5248727674.0,44480743.0,GSM7092951 r4,0:28 1:90,A:1410656147;C:1249808557;G:1244236491;T:1343925912;N:100567,28,90,,,1410656147,1249808557,1244236491,1343925912,100567,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00445,0.86738,0.0013,0.06588,0.99297,0.8423,0.42409,0.57081,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74500,SRR23824342,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L001_R2_001.fastq.gz 7dpi-WKM-1_S18_L001_R1_001.fastq.gz,fastq fastq,4614142082.0,39102899.0,GSM7092950 r1,0:28 1:90,A:1221539435;C:1116323438;G:1093348138;T:1182827232;N:103839,28,90,,,1221539435,1116323438,1093348138,1182827232,103839,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00406,0.85345,0.00122,0.05709,0.99395,0.84804,0.43589,0.58021,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74501,SRR23824343,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L002_R1_001.fastq.gz 7dpi-WKM-1_S18_L002_R2_001.fastq.gz,fastq fastq,4593976590.0,38932005.0,GSM7092950 r2,0:28 1:90,A:1215610872;C:1111440315;G:1088719031;T:1178107008;N:99364,28,90,,,1215610872,1111440315,1088719031,1178107008,99364,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00457,0.85489,0.00152,0.0572,0.99348,0.84893,0.35025,0.57809,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74502,SRR23824352,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L003_R1_001.fastq.gz 7dpi-WKM-1_S18_L003_R2_001.fastq.gz,fastq fastq,4683123702.0,39687489.0,GSM7092950 r3,0:28 1:90,A:1239167418;C:1133378913;G:1110025813;T:1200456657;N:94901,28,90,,,1239167418,1133378913,1110025813,1200456657,94901,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00461,0.85316,0.00136,0.05779,0.99342,0.84879,0.45151,0.57995,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74503,SRR23824353,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L004_R2_001.fastq.gz 7dpi-WKM-1_S18_L004_R1_001.fastq.gz,fastq fastq,4592030652.0,38915514.0,GSM7092950 r4,0:28 1:90,A:1215524167;C:1110582945;G:1087749475;T:1178087315;N:86750,28,90,,,1215524167,1110582945,1087749475,1178087315,86750,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00436,0.85419,0.00129,0.05769,0.99373,0.84774,0.37268,0.58314,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74528,SRR23824372,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L001_R1_001.fastq.gz 1dpi-WKM-2_S14_L001_R2_001.fastq.gz,fastq fastq,4503800990.0,38167805.0,GSM7092943 r1,0:28 1:90,A:1248352720;C:1030070974;G:1053667995;T:1171606946;N:102355,28,90,,,1248352720,1030070974,1053667995,1171606946,102355,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00404,0.88157,0.00136,0.10856,0.99316,0.81615,0.4,0.55334,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74529,SRR23824373,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L002_R1_001.fastq.gz 1dpi-WKM-2_S14_L002_R2_001.fastq.gz,fastq fastq,4531566744.0,38403108.0,GSM7092943 r2,0:28 1:90,A:1255485872;C:1036592881;G:1060058376;T:1179332155;N:97460,28,90,,,1255485872,1036592881,1060058376,1179332155,97460,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00412,0.88028,0.00143,0.10789,0.99269,0.81779,0.43243,0.55729,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74530,SRR23824386,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L003_R1_001.fastq.gz 1dpi-WKM-2_S14_L003_R2_001.fastq.gz,fastq fastq,4578982212.0,38804934.0,GSM7092943 r3,0:28 1:90,A:1268278355;C:1047870699;G:1071633982;T:1191106598;N:92578,28,90,,,1268278355,1047870699,1071633982,1191106598,92578,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00402,0.88112,0.00132,0.10858,0.99273,0.81744,0.37667,0.55459,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system