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
11017,ERR9750937,ERX9298876,ERS12023662,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Uninjured,SAMEA14418104,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418104|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 2 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Uninjured p,Expt 2 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9325673775.0,69079065.0,E MTAB 10643:Expt 2 Uninjured,0:10 1:10 2:28 3:87,A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294,10,10,28,87,1619571910,1420805235,1471531128,1496998088,972294,ERX9298876,ERS12023662,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.93798,,0.11364,,0.84843,,0.53531,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11018,ERR9750936,ERX9298875,ERS12023661,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Sham,SAMEA14418103,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418103|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Sham|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:sham surgery|organism part:heart|sample name:E MTAB 10643:Expt 2 Sham|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Sham p,Expt 2 Sham p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:sham surgery|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11328674040.0,83916104.0,E MTAB 10643:Expt 2 Sham,0:10 1:10 2:28 3:87,A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102,10,10,28,87,1955327720,1746332187,1777122701,1820705338,1213102,ERX9298875,ERS12023661,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92847,,0.09981,,0.85707,,0.46947,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11019,ERR9750935,ERX9298874,ERS12023660,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 3d post amputation,SAMEA14418102,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 3d post amputation p,Expt 2 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,16111486440.0,119344344.0,E MTAB 10643:Expt 2 3d post amputation,0:10 1:10 2:28 3:87,A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227,10,10,28,87,2610144058,2617445332,2496763759,2656876552,1728227,ERX9298874,ERS12023660,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.94868,,0.07071,,0.89221,,0.54333,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11020,ERR9750934,ERX9298873,ERS12023659,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 3 3d post amputation + MMP inhibitor,SAMEA14418101,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418101|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|sex:male|strain:AB|treatment:matrix metalloproteinase inhibitor,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p,Expt 3 3d post amputation + MMP inhibitor p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:matrix metalloproteinase inhibitor,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8621019270.0,63859402.0,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor,0:10 1:10 2:28 3:87,A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502,10,10,28,87,1438763050,1365497247,1350808021,1399773154,926502,ERX9298873,ERS12023659,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92796,,0.08671,,0.87176,,0.55088,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11021,ERR9750933,ERX9298872,ERS12023658,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 Uninjured,SAMEA14418100,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418100|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 Uninjured p,Expt 1 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz,fastq fastq fastq,8575585211.0,67524293.0,E MTAB 10643:Expt 1 Uninjured,0:8 1:28 2:91,A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801,8,28,91,,1801503847,1312196506,1367890726,1663053783,65801,ERX9298872,ERS12023658,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.9169,,0.11202,,0.81576,,0.54253,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11022,ERR9750932,ERX9298871,ERS12023657,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 7d post amputation,SAMEA14418099,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418099|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 7d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 7d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 7d post amputation p,Expt 1 7d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:7|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz,fastq fastq fastq,17341796660.0,136549580.0,E MTAB 10643:Expt 1 7d post amputation,0:8 1:28 2:91,A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162,8,28,91,,3506600812,2774617588,2814960106,3329701112,132162,ERX9298871,ERS12023657,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90616,,0.09608,,0.82446,,0.46632,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11023,ERR9750931,ERX9298870,ERS12023656,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 3d post amputation,SAMEA14418098,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418098|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 3d post amputation p,Expt 1 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz,fastq fastq fastq,8183008018.0,64433134.0,E MTAB 10643:Expt 1 3d post amputation,0:8 1:28 2:91,A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630,8,28,91,,1630460899,1330248096,1326144211,1576499358,62630,ERX9298870,ERS12023656,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.88759,,0.08679,,0.82948,,0.47863,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11024,ERR9750930,ERX9298869,ERS12023655,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 14d post amputation,SAMEA14418097,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418097|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 14d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 14d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 14d post amputation p,Expt 1 14d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:14|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz,fastq fastq fastq,12911908390.0,101668570.0,E MTAB 10643:Expt 1 14d post amputation,0:8 1:28 2:91,A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857,8,28,91,,2700371496,1971281481,2062280628,2517806408,99857,ERX9298869,ERS12023655,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90771,,0.11048,,0.81523,,0.53024,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
26482,SRR25930974,SRX21649989,SRS18818461,SRP458853,PRJNA1013567,scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts,GSE242483,Transcriptome Analysis,Seeking to identify additional transcription factors required for cardiac valve formation  we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established  and at 80 hpf when forming valves are first observed,,pubmed:38748804,,80hpf,GSM7764482,,source name:heart|tissue:heart|genotype:wild type|age:80hpf|geo loc name:missing|collection date:missing,80hpf,Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore  we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs,heart,,Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000,,tissue:heart|genotype:wild type|age:80hpf,GSM7764482,GSM7764482: 80hpf; Danio rerio; RNA Seq,GSM7764482 r1,GSM7764482,1,Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP458853,,,Giulia_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz,fastq fastq,18811433188.0,225273324.0,GSM7764482 r1,0:28 1:55.50,A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878,28,55,,,5135587480,4020079745,4129712330,5427444755,98608878,SRX21649989,SRS18818461,SRA1706674,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",2,0.00187,0.93611,0.00071,0.16105,0.99626,0.79825,0.41545,0.50249,28,55,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-09-06,Larval,Larval,Heart,Cardiovascular System
26483,SRR25930975,SRX21649988,SRS18818460,SRP458853,PRJNA1013567,scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts,GSE242483,Transcriptome Analysis,Seeking to identify additional transcription factors required for cardiac valve formation  we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established  and at 80 hpf when forming valves are first observed,,pubmed:38748804,,50hpf,GSM7764481,,source name:heart|tissue:heart|genotype:wild type|age:50hpf|geo loc name:missing|collection date:missing,50hpf,Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore  we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs,heart,,Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000,,tissue:heart|genotype:wild type|age:50hpf,GSM7764481,GSM7764481: 50hpf; Danio rerio; RNA Seq,GSM7764481 r1,GSM7764481,1,Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP458853,,,Giulia_50hpf_S1_R2_001.fastq.gz Giulia_50hpf_S1_R1_001.fastq.gz,fastq fastq,19874763820.0,237988724.0,GSM7764481 r1,0:28 1:55.51,A:5320257914;C:4424267230;G:4320623789;T:5708249185;N:101365702,28,55,,,5320257914,4424267230,4320623789,5708249185,101365702,SRX21649988,SRS18818460,SRA1706674,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",2,0.00185,0.94414,0.00087,0.13397,0.99675,0.80172,0.41142,0.51985,28,56,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-09-06,Hatching,Embryo,Heart,Cardiovascular System
28771,SRR26639098,SRX22339478,SRS19389127,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,sibling  replicate 2  snRNAseq,GSM7880035,,source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing,sibling  replicate 2  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:wt sibling,GSM7880035,GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq,GSM7880035 r1,GSM7880035,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,sib_2_S1_L001_R1_001.fastq.gz sib_2_S1_L001_R2_001.fastq.gz,fastq fastq,29585942468.0,250728326.0,GSM7880035 r1,0:29 1:89,A:8869085825;C:6519678188;G:6681924988;T:7515095066;N:158401,29,89,,,8869085825,6519678188,6681924988,7515095066,158401,SRX22339478,SRS19389127,SRA1744308,University of Bern,University of Bern,2,0.03708,0.89742,0.02638,0.33817,0.98766,0.87265,0.50529,0.84547,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28772,SRR26639099,SRX22339478,SRS19389127,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,sibling  replicate 2  snRNAseq,GSM7880035,,source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing,sibling  replicate 2  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:wt sibling,GSM7880035,GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq,GSM7880035 r1,GSM7880035,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz,fastq fastq,29238445684.0,247783438.0,GSM7880035 r2,0:29 1:89,A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758,29,89,,,8764474921,6441070570,6601843083,7430828352,228758,SRX22339478,SRS19389127,SRA1744308,University of Bern,University of Bern,2,0.03758,0.89628,0.02664,0.33912,0.98711,0.87442,0.4887,0.42456,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28773,SRR26639100,SRX22339477,SRS19389126,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,sibling  replicate 1  snRNAseq,GSM7880034,,source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing,sibling  replicate 1  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:wt sibling,GSM7880034,GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq,GSM7880034 r1,GSM7880034,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,sib_1_S1_L001_R1_001.fastq.gz sib_1_S1_L001_R2_001.fastq.gz,fastq fastq,24652163520.0,208916640.0,GSM7880034 r1,0:29 1:89,A:7206225437;C:5487875216;G:5870141423;T:6087790451;N:130993,29,89,,,7206225437,5487875216,5870141423,6087790451,130993,SRX22339477,SRS19389126,SRA1744308,University of Bern,University of Bern,2,0.04136,0.8662,0.02868,0.3899,0.98597,0.86906,0.42284,0.79265,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28774,SRR26639101,SRX22339477,SRS19389126,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,sibling  replicate 1  snRNAseq,GSM7880034,,source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing,sibling  replicate 1  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:wt sibling,GSM7880034,GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq,GSM7880034 r1,GSM7880034,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,sib_1_S1_L002_R1_001.fastq.gz sib_1_S1_L002_R2_001.fastq.gz,fastq fastq,24333156656.0,206213192.0,GSM7880034 r2,0:29 1:89,A:7112369699;C:5414867956;G:5792728480;T:6013000607;N:189914,29,89,,,7112369699,5414867956,5792728480,6013000607,189914,SRX22339477,SRS19389126,SRA1744308,University of Bern,University of Bern,2,0.04141,0.86578,0.02866,0.39157,0.98614,0.8704,0.42701,0.78792,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28775,SRR26639102,SRX22339476,SRS19389125,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,spns mutant  replicate 2  snRNAseq,GSM7880033,,source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing,spns mutant  replicate 2  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:spns mutant,GSM7880033,GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq,GSM7880033 r1,GSM7880033,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,mut_2_S1_L001_R1_001.fastq.gz mut_2_S1_L001_R2_001.fastq.gz,fastq fastq,33067082062.0,280229509.0,GSM7880033 r1,0:29 1:89,A:9837791085;C:7302189072;G:7479072379;T:8447851569;N:177957,29,89,,,9837791085,7302189072,7479072379,8447851569,177957,SRX22339476,SRS19389125,SRA1744308,University of Bern,University of Bern,2,0.03975,0.89392,0.02827,0.35098,0.98693,0.87572,0.42665,0.8308,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28776,SRR26639103,SRX22339476,SRS19389125,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,spns mutant  replicate 2  snRNAseq,GSM7880033,,source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing,spns mutant  replicate 2  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:spns mutant,GSM7880033,GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq,GSM7880033 r1,GSM7880033,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,mut_2_S1_L002_R1_001.fastq.gz mut_2_S1_L002_R2_001.fastq.gz,fastq fastq,32794778418.0,277921851.0,GSM7880033 r2,0:29 1:89,A:9757463504;C:7238976466;G:7415128557;T:8382951671;N:258220,29,89,,,9757463504,7238976466,7415128557,8382951671,258220,SRX22339476,SRS19389125,SRA1744308,University of Bern,University of Bern,2,0.04055,0.89543,0.02892,0.35129,0.98654,0.87655,0.45394,0.85056,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28777,SRR26639104,SRX22339475,SRS19389124,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,spns mutant  replicate 1  snRNAseq,GSM7880032,,source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing,spns mutant  replicate 1  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:spns mutant,GSM7880032,GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq,GSM7880032 r1,GSM7880032,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz,fastq fastq,30027997254.0,254474553.0,GSM7880032 r1,0:29 1:89,A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572,29,89,,,9128230353,6473885422,6895366272,7530354635,160572,SRX22339475,SRS19389124,SRA1744308,University of Bern,University of Bern,2,0.03908,0.86231,0.0274,0.38263,0.98701,0.87113,0.48114,0.78783,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
28778,SRR26639105,SRX22339475,SRS19389124,SRP469857,PRJNA1034995,Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.,GSE246850,Transcriptome Analysis,Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.,,pubmed:39720516,,spns mutant  replicate 1  snRNAseq,GSM7880032,,source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing,spns mutant  replicate 1  snRNAseq,The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix,heart,,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,tissue:heart|age:3dpf|genotype:spns mutant,GSM7880032,GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq,GSM7880032 r1,GSM7880032,1,Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described​65​. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80° C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469857,,loader:fastq load.py,mut_1_S1_L002_R1_001.fastq.gz mut_1_S1_L002_R2_001.fastq.gz,fastq fastq,29506651188.0,250056366.0,GSM7880032 r2,0:29 1:89,A:8967217701;C:6359649244;G:6775979696;T:7403576105;N:228442,29,89,,,8967217701,6359649244,6775979696,7403576105,228442,SRX22339475,SRS19389124,SRA1744308,University of Bern,University of Bern,2,0.03885,0.86188,0.02749,0.38666,0.98644,0.86975,0.46306,0.79451,29,89,T,B,sc-like readlen,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-11-02,Larval,Larval,Heart,Cardiovascular System
29201,SRR27319715,SRX22996941,SRS19961590,SRP479504,PRJNA1055557,Border zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration,GSE251856,Other,Despite numerous advances in our understanding of zebrafish cardiac regeneration  an aspect that remains less studied is how newly proliferated cardiomyocytes invade  and eventually replace  the collagen containing fibrotic tissue following injury.  Here  we provide an in depth analysis of the process of cardiomyocyte invasion and migration using live imaging and histological approaches.  We observed a close interaction between protruding cardiomyocytes and macrophages at the wound border zone  and irf8 mutant zebrafish  which largely lack macrophages  exhibited defects in extracellular matrix ECM remodeling and cardiomyocyte protrusion into the injured area.  Using a resident macrophage ablation model  we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages.  Single cell RNA sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast like gene expression signatures  including the expression of genes encoding ECM structural proteins and ECM remodeling proteins.  The expression of mmp14b  which encodes a membrane anchored matrix metalloproteinase  was restricted to cells in the border zone and genetic deletion of mmp14b led to a decrease in 1 collagen degradation at the border zone  2 macrophage recruitment to the border zone  and 3 subsequent cardiomyocyte invasion.  Furthermore  cardiomyocyte specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion both into the injured area and along the apical surface of the wound.  Altogether  our data shed important insights into the process of cardiomyocyte invasion of the collagen containing injured tissue during cardiac regeneration.  They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue. Overall design: The border zone of regenerating wild type zebrafish hearts at 7 dpci was microdissected and subjected to scRNA seq,,pubmed:39962064;pubmed:40268967,,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,GSM7989198,,source name:Heart|tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq|geo loc name:missing|collection date:missing,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 23 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore  we filtered 9874 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs,Heart,Zebrafish hearts were cryoinjured and extracted at 7 dpci.,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq,GSM7989198,GSM7989198: scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci; Danio rerio; RNA Seq,GSM7989198 r1,GSM7989198,1,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer's protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP479504,,,Arica_10x_Zebrafish_Borderzone_Lib_R2.fastq.gz Arica_10x_Zebrafish_Borderzone_Lib_R1.fastq.gz,fastq fastq,35579193737.0,447572139.0,GSM7989198 r1,0:28 1:51.49,A:9662436792;C:7884457111;G:8055970010;T:9787114480;N:189215344,28,51,,,9662436792,7884457111,8055970010,9787114480,189215344,SRX22996941,SRS19961590,SRA1774131,MPI for heart and lung research,MPI for heart and lung research,2,0.00237,0.94011,0.00086,0.09945,0.99571,0.81907,0.32746,0.60892,28,51,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Heart,Cardiovascular System
30738,SRR28346485,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  IWR1  scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC  IWR1  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC  IWR1  scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L001_I1_001.fastq.gz AVC_IWR1_S1_L001_I2_001.fastq.gz AVC_IWR1_S1_L001_R1_001.fastq.gz AVC_IWR1_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8596842480.0,62295960.0,GSM8147318 r1,0:10 1:10 2:28 3:90,A:1570400090;C:1308581548;G:1326249813;T:1399966642;N:1438307,10,10,28,90,1570400090,1308581548,1326249813,1399966642,1438307,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30739,SRR28346486,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  IWR1  scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC  IWR1  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC  IWR1  scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L002_I1_001.fastq.gz AVC_IWR1_S1_L002_I2_001.fastq.gz AVC_IWR1_S1_L002_R1_001.fastq.gz AVC_IWR1_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8505185502.0,61631779.0,GSM8147318 r2,0:10 1:10 2:28 3:90,A:1553616390;C:1294687778;G:1312612882;T:1384504011;N:1439049,10,10,28,90,1553616390,1294687778,1312612882,1384504011,1439049,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30740,SRR28346487,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  IWR1  scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC  IWR1  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC  IWR1  scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L003_I1_001.fastq.gz AVC_IWR1_S1_L003_I2_001.fastq.gz AVC_IWR1_S1_L003_R1_001.fastq.gz AVC_IWR1_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8699205498.0,63037721.0,GSM8147318 r3,0:10 1:10 2:28 3:90,A:1588465122;C:1324147204;G:1343996634;T:1415623074;N:1162856,10,10,28,90,1588465122,1324147204,1343996634,1415623074,1162856,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30741,SRR28346488,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  IWR1  scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC  IWR1  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC  IWR1  scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L004_I1_001.fastq.gz AVC_IWR1_S1_L004_I2_001.fastq.gz AVC_IWR1_S1_L004_R1_001.fastq.gz AVC_IWR1_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8627728812.0,62519774.0,GSM8147318 r4,0:10 1:10 2:28 3:90,A:1576009383;C:1313466786;G:1332114241;T:1404392019;N:797231,10,10,28,90,1576009383,1313466786,1332114241,1404392019,797231,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30742,SRR28346489,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  DMSO  scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L001_I1_001.fastq.gz AVC_Ctrl_S1_L001_I2_001.fastq.gz AVC_Ctrl_S1_L001_R1_001.fastq.gz AVC_Ctrl_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,7385103810.0,53515245.0,GSM8147317 r1,0:10 1:10 2:28 3:90,A:1329371520;C:1135299252;G:1143250549;T:1207226310;N:1224419,10,10,28,90,1329371520,1135299252,1143250549,1207226310,1224419,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30743,SRR28346490,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  DMSO  scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L002_I1_001.fastq.gz AVC_Ctrl_S1_L002_I2_001.fastq.gz AVC_Ctrl_S1_L002_R1_001.fastq.gz AVC_Ctrl_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,7313299098.0,52994921.0,GSM8147317 r2,0:10 1:10 2:28 3:90,A:1316101332;C:1124200896;G:1133146934;T:1194866024;N:1227704,10,10,28,90,1316101332,1124200896,1133146934,1194866024,1227704,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30744,SRR28346491,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  DMSO  scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L003_I1_001.fastq.gz AVC_Ctrl_S1_L003_I2_001.fastq.gz AVC_Ctrl_S1_L003_R1_001.fastq.gz AVC_Ctrl_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,7457857272.0,54042444.0,GSM8147317 r3,0:10 1:10 2:28 3:90,A:1341763332;C:1146520201;G:1156131488;T:1218395804;N:1009135,10,10,28,90,1341763332,1146520201,1156131488,1218395804,1009135,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30745,SRR28346492,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs  we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month  which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling  we also collected AVC from fish treated with DMSO or IWR1 endo  an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO  respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC  DMSO  scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected in low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L004_I1_001.fastq.gz AVC_Ctrl_S1_L004_I2_001.fastq.gz AVC_Ctrl_S1_L004_R1_001.fastq.gz AVC_Ctrl_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,7430049030.0,53840935.0,GSM8147317 r4,0:10 1:10 2:28 3:90,A:1337094348;C:1142353903;G:1151539276;T:1214006711;N:689912,10,10,28,90,1337094348,1142353903,1151539276,1214006711,689912,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30746,SRR28348607,SRX23954674,SRS20755104,SRP495302,PRJNA1088122,Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system,GSE261619,Transcriptome Analysis,In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.,,pubmed:39632839,,Tgelavl3:eGFP  Tgnbt:DsRed,GSM8147512,,source name:atrium|tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed|geo loc name:missing|collection date:missing,Tgelavl3:eGFP  Tgnbt:DsRed,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,atrium,,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed,GSM8147512,GSM8147512: Tgelavl3:eGFP  Tgnbt:DsRed; Danio rerio; RNA Seq,GSM8147512 r1,GSM8147512,1,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495302,,loader:fastq load.py,CP030_S1_L004_I1_001.fastq.gz CP030_S1_L004_I2_001.fastq.gz CP030_S1_L004_R1_001.fastq.gz CP030_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,86914563102.0,391507041.0,GSM8147512 r1,0:10 1:10 2:101 3:101,A:23707102309;C:15625825731;G:14915197158;T:24834868356;N:1428728,10,10,101,101,23707102309,15625825731,14915197158,24834868356,1428728,SRX23954674,SRS20755104,SRA1824602,"Neurology &amp; TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.0,0.94374,0.0,0.12308,1.0,0.82055,,0.55544,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-14,Undetermined,Adult,Heart,Cardiovascular System
30747,SRR28348608,SRX23954673,SRS20755103,SRP495302,PRJNA1088122,Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system,GSE261619,Transcriptome Analysis,In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.,,pubmed:39632839,,Tgelavl3:eGFP,GSM8147511,,source name:whole heart|tissue:whole heart|genotype:Tgelavl3:eGFP|geo loc name:missing|collection date:missing,Tgelavl3:eGFP,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,whole heart,,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:whole heart|genotype:Tgelavl3:eGFP,GSM8147511,GSM8147511: Tgelavl3:eGFP; Danio rerio; RNA Seq,GSM8147511 r1,GSM8147511,1,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495302,,loader:fastq load.py,CP017_S1_L001_I1_001.fastq.gz CP017_S1_L001_I2_001.fastq.gz CP017_S1_L001_R1_001.fastq.gz CP017_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,41176621272.0,185480276.0,GSM8147511 r1,0:10 1:10 2:101 3:101,A:9993088511;C:6520920913;G:6513822557;T:14438876590;N:307181,10,10,101,101,9993088511,6520920913,6513822557,14438876590,307181,SRX23954673,SRS20755103,SRA1824602,"Neurology &amp; TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.01251,0.96696,0.0018,0.07994,0.9922,0.83861,0.46366,0.47886,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-14,Undetermined,Adult,Heart,Cardiovascular System
30748,SRR28348609,SRX23954673,SRS20755103,SRP495302,PRJNA1088122,Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system,GSE261619,Transcriptome Analysis,In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.,,pubmed:39632839,,Tgelavl3:eGFP,GSM8147511,,source name:whole heart|tissue:whole heart|genotype:Tgelavl3:eGFP|geo loc name:missing|collection date:missing,Tgelavl3:eGFP,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,whole heart,,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:whole heart|genotype:Tgelavl3:eGFP,GSM8147511,GSM8147511: Tgelavl3:eGFP; Danio rerio; RNA Seq,GSM8147511 r1,GSM8147511,1,Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495302,,loader:fastq load.py,CP017_S1_L002_I1_001.fastq.gz CP017_S1_L002_I2_001.fastq.gz CP017_S1_L002_R1_001.fastq.gz CP017_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,41449667730.0,186710215.0,GSM8147511 r2,0:10 1:10 2:101 3:101,A:10111586707;C:6536521889;G:6498472573;T:14568538148;N:344113,10,10,101,101,10111586707,6536521889,6498472573,14568538148,344113,SRX23954673,SRS20755103,SRA1824602,"Neurology &amp; TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.01136,0.96721,0.00127,0.07919,0.99299,0.83956,0.4846,0.4789,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-14,Undetermined,Adult,Heart,Cardiovascular System
30775,SRR28357669,SRX23962905,SRS20762620,SRP495490,PRJNA1088483,Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA Seq],GSE261718,Other,Purpose: To explore the endogenous expression pattern of Erbb2. Methods:  Approximately 1000 hearts dissected from 72 hpf Tgmyl7:mCherry embryos were digested in 0.25% trypsin EDTA solution for single cell RNA sequencing. Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2  but weakly expressed in subcluster 3  10 and 12. Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation. Overall design: 72 hpf Tgmyl7:mCherry zebrafish hearts were collected for single cell RNA sequencing.,,pubmed:40053597,,S72hpf trunks,GSM8149579,,source name:zebrafish hearts|tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells|geo loc name:missing|collection date:missing,S72hpf trunks,Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: zip compressed  files include filtered gene bc matrices post running CellRanger pipeline,zebrafish hearts,,A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer’s instructions. Single cell RNA Seq 10x,Dechorionated zebrafish embryos were maintained in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h light/dark.,tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells,GSM8149579,GSM8149579: S72hpf trunks; Danio rerio; RNA Seq,GSM8149579 r1,GSM8149579,1,A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer's instructions. Single cell RNA Seq 10x,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495490,,,zebrafish_heart_72h_R1_fastq.gz zebrafish_heart_72h_R2_fastq.gz,fastq fastq,155978889600.0,519929632.0,GSM8149579 r1,0:150 1:150,A:63302225780;C:28042347630;G:26792086978;T:37838422350;N:3806862,150,150,,,63302225780,28042347630,26792086978,37838422350,3806862,SRX23962905,SRS20762620,SRA1825277,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",2,0.0,0.92044,0.0,0.11022,1.0,0.80996,,0.54499,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-03-15,Larval,Larval,Heart,Cardiovascular System
31528,SRR28423881,SRX24027916,SRS20821688,SRP497294,PRJNA1090898,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst169,GSE262247,Transcriptome Analysis,The innate immune system is triggered xxx post injury and its spatiotemporal dynamics are critical for successful regeneration.  MyD88 is a key component of the innate immune response; however  its role during regeneration remains unclear.  Here we show that MyD88 controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  Our data reveal a significant reduction in pro inflammatory neutrophil and macrophage populations  as well as the expansion of a collagen rich endocardial population in cryoinjured myd88 /  ventricles.  Consistent with these findings  we observed increased myofibroblasts  fibrin abundance  and scarring in myd88 /  ventricles.  Transcriptomic analyses of endocardial cells and immunostaining experiments reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium.  Moreover  loss of MyD88 impairs cardiomyocyte proliferation and protrusive activity towards the injured area.  Notably  endothelial specific overexpression of myd88 reverses the neutrophil  fibrotic  and scarring phenotypes in cryoinjured myd88 /  ventricles.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a transcriptional target of the MyD88 signaling axis and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis  thereby emphasizing the strong impact of the innate immune response during tissue regeneration. Overall design: Live zebrafish ventricular cells were isolated at 24 hour post cryoinjury hpci from myd88+/+ and myd88 /  ventricles by Fluorescence activated cell sorting FACS and analyzed using scRNAseq.,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricular cells  myd88 /   24 hpci,GSM8161054,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,ventricular cells  myd88 /   24 hpci,Raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Dobin et al.  doi: 10.1093/bioinformatics/bts635 followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy Wolf et al.  doi: 10.1186/s13059 017 1382 0. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 32 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 10%. Furthermore  we filtered 7823 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection Traag et al.  https://arxiv.org/abs/1810.08473  were based on the initial PCA. Final data visualization was done by CellxGene package DOI 10.5281/zenodo.3235020. Assembly: DanRer11 Supplementary files format and content: starsolo outputs,cardiac ventricles,cardiac cryoinjury 24 hours prior to heart extraction,Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer’s instructions and with the following modifications: Incubation was performed at 30°C for 20 min  followed by resuspension in 1× Hanks’ balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell 3’ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury,GSM8161054,GSM8161054: ventricular cells  myd88 /   24 hpci; Danio rerio; RNA Seq,GSM8161054 r1,GSM8161054,1,Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer's instructions and with the following modifications: Incubation was performed at 30°C for 20 min  followed by resuspension in 1× Hanks' balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP497294,,,Pinelopi_10x_Zebrafish_Mut_Lib_R1.fastq.gz Pinelopi_10x_Zebrafish_Mut_Lib_R2.fastq.gz,fastq fastq,31356990530.0,394538049.0,GSM8161054 r1,0:28 1:51.48,A:8573180857;C:6884590114;G:7520784498;T:8220228225;N:158206836,28,51,,,8573180857,6884590114,7520784498,8220228225,158206836,SRX24027916,SRS20821688,SRA1832827,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2024-03-22,Cleavage,Embryo,Heart,Cardiovascular System
31529,SRR28423882,SRX24027915,SRS20821687,SRP497294,PRJNA1090898,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst169,GSE262247,Transcriptome Analysis,The innate immune system is triggered xxx post injury and its spatiotemporal dynamics are critical for successful regeneration.  MyD88 is a key component of the innate immune response; however  its role during regeneration remains unclear.  Here we show that MyD88 controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  Our data reveal a significant reduction in pro inflammatory neutrophil and macrophage populations  as well as the expansion of a collagen rich endocardial population in cryoinjured myd88 /  ventricles.  Consistent with these findings  we observed increased myofibroblasts  fibrin abundance  and scarring in myd88 /  ventricles.  Transcriptomic analyses of endocardial cells and immunostaining experiments reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium.  Moreover  loss of MyD88 impairs cardiomyocyte proliferation and protrusive activity towards the injured area.  Notably  endothelial specific overexpression of myd88 reverses the neutrophil  fibrotic  and scarring phenotypes in cryoinjured myd88 /  ventricles.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a transcriptional target of the MyD88 signaling axis and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis  thereby emphasizing the strong impact of the innate immune response during tissue regeneration. Overall design: Live zebrafish ventricular cells were isolated at 24 hour post cryoinjury hpci from myd88+/+ and myd88 /  ventricles by Fluorescence activated cell sorting FACS and analyzed using scRNAseq.,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricular cells  myd88+/+  24 hpci,GSM8161053,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,ventricular cells  myd88+/+  24 hpci,Raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Dobin et al.  doi: 10.1093/bioinformatics/bts635 followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy Wolf et al.  doi: 10.1186/s13059 017 1382 0. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 32 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 10%. Furthermore  we filtered 7823 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection Traag et al.  https://arxiv.org/abs/1810.08473  were based on the initial PCA. Final data visualization was done by CellxGene package DOI 10.5281/zenodo.3235020. Assembly: DanRer11 Supplementary files format and content: starsolo outputs,cardiac ventricles,cardiac cryoinjury 24 hours prior to heart extraction,Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer’s instructions and with the following modifications: Incubation was performed at 30°C for 20 min  followed by resuspension in 1× Hanks’ balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell 3’ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury,GSM8161053,GSM8161053: ventricular cells  myd88+/+  24 hpci; Danio rerio; RNA Seq,GSM8161053 r1,GSM8161053,1,Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer's instructions and with the following modifications: Incubation was performed at 30°C for 20 min  followed by resuspension in 1× Hanks' balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP497294,,,Pinelopi_10x_Zebrafish_WT_Lib_R1.fastq.gz Pinelopi_10x_Zebrafish_WT_Lib_R2.fastq.gz,fastq fastq,40672259373.0,511650018.0,GSM8161053 r1,0:28 1:51.49,A:11079272327;C:8809520398;G:9307205642;T:11269370263;N:206890743,28,51,,,11079272327,8809520398,9307205642,11269370263,206890743,SRX24027915,SRS20821687,SRA1832827,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2024-03-22,Cleavage,Embryo,Heart,Cardiovascular System
31674,SRR28490919,SRX24093157,SRS20882453,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep6,GSM8173843,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep6,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173843,GSM8173843: zebrafish 14dpi rep6; Danio rerio; RNA Seq,GSM8173843 r1,GSM8173843,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19730X3 220617 A00421 0450 BHYLWFDSX3 S12 L004 I1 001.fastq.gz   read2PairFiles=19730X3 220617 A00421 0450 BHYLWFDSX3 S12 L004 I2 001.fastq.gz   read3PairFiles=19730X3 220617 A00421 0450 BHYLWFDSX3 S12 L004 R1 001.fastq.gz   read4PairFiles=19730X3 220617 A00421 0450 BHYLWFDSX3 S12 L004 R2 001.fastq.gz,19730X3_220617_A00421_0450_BHYLWFDSX3_S12_L004_I1_001.fastq.gz 19730X3_220617_A00421_0450_BHYLWFDSX3_S12_L004_I2_001.fastq.gz 19730X3_220617_A00421_0450_BHYLWFDSX3_S12_L004_R1_001.fastq.gz 19730X3_220617_A00421_0450_BHYLWFDSX3_S12_L004_R2_001.fastq.gz,fastq fastq fastq fastq,74593926792.0,376737004.0,GSM8173843 r1,0:10 1:10 2:28 3:150,A:19954586491;C:15851545871;G:13974009323;T:17278682199;N:362828,10,10,28,150,19954586491,15851545871,13974009323,17278682199,362828,SRX24093157,SRS20882453,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31675,SRR28490920,SRX24093156,SRS20882452,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep5,GSM8173842,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep5,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173842,GSM8173842: zebrafish 14dpi rep5; Danio rerio; RNA Seq,GSM8173842 r1,GSM8173842,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19730X2 220617 A00421 0450 BHYLWFDSX3 S11 L004 I1 001.fastq.gz   read2PairFiles=19730X2 220617 A00421 0450 BHYLWFDSX3 S11 L004 I2 001.fastq.gz   read3PairFiles=19730X2 220617 A00421 0450 BHYLWFDSX3 S11 L004 R1 001.fastq.gz   read4PairFiles=19730X2 220617 A00421 0450 BHYLWFDSX3 S11 L004 R2 001.fastq.gz,19730X2_220617_A00421_0450_BHYLWFDSX3_S11_L004_I1_001.fastq.gz 19730X2_220617_A00421_0450_BHYLWFDSX3_S11_L004_I2_001.fastq.gz 19730X2_220617_A00421_0450_BHYLWFDSX3_S11_L004_R1_001.fastq.gz 19730X2_220617_A00421_0450_BHYLWFDSX3_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq,74566602396.0,376599002.0,GSM8173842 r1,0:10 1:10 2:28 3:150,A:20294748919;C:15450598433;G:14469235760;T:16819675865;N:363379,10,10,28,150,20294748919,15450598433,14469235760,16819675865,363379,SRX24093156,SRS20882452,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31676,SRR28490921,SRX24093155,SRS20882451,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep4,GSM8173841,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep4,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173841,GSM8173841: zebrafish 14dpi rep4; Danio rerio; RNA Seq,GSM8173841 r1,GSM8173841,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19730X1 220617 A00421 0450 BHYLWFDSX3 S10 L004 I1 001.fastq.gz   read2PairFiles=19730X1 220617 A00421 0450 BHYLWFDSX3 S10 L004 I2 001.fastq.gz   read3PairFiles=19730X1 220617 A00421 0450 BHYLWFDSX3 S10 L004 R1 001.fastq.gz   read4PairFiles=19730X1 220617 A00421 0450 BHYLWFDSX3 S10 L004 R2 001.fastq.gz,19730X1_220617_A00421_0450_BHYLWFDSX3_S10_L004_I1_001.fastq.gz 19730X1_220617_A00421_0450_BHYLWFDSX3_S10_L004_I2_001.fastq.gz 19730X1_220617_A00421_0450_BHYLWFDSX3_S10_L004_R1_001.fastq.gz 19730X1_220617_A00421_0450_BHYLWFDSX3_S10_L004_R2_001.fastq.gz,fastq fastq fastq fastq,76061576646.0,384149377.0,GSM8173841 r1,0:10 1:10 2:28 3:150,A:19982364126;C:15578867054;G:15092653159;T:17724332310;N:372457,10,10,28,150,19982364126,15578867054,15092653159,17724332310,372457,SRX24093155,SRS20882451,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31677,SRR28490922,SRX24093154,SRS20882450,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep3,GSM8173840,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep3,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173840,GSM8173840: zebrafish 14dpi rep3; Danio rerio; RNA Seq,GSM8173840 r1,GSM8173840,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19495X3 220201 A00421 0414 BH7MJYDSX3 S9 L004 I1 001.fastq.gz   read2PairFiles=19495X3 220201 A00421 0414 BH7MJYDSX3 S9 L004 I2 001.fastq.gz   read3PairFiles=19495X3 220201 A00421 0414 BH7MJYDSX3 S9 L004 R1 001.fastq.gz   read4PairFiles=19495X3 220201 A00421 0414 BH7MJYDSX3 S9 L004 R2 001.fastq.gz,19495X3_220201_A00421_0414_BH7MJYDSX3_S9_L004_I1_001.fastq.gz 19495X3_220201_A00421_0414_BH7MJYDSX3_S9_L004_I2_001.fastq.gz 19495X3_220201_A00421_0414_BH7MJYDSX3_S9_L004_R1_001.fastq.gz 19495X3_220201_A00421_0414_BH7MJYDSX3_S9_L004_R2_001.fastq.gz,fastq fastq fastq fastq,94197045690.0,475742655.0,GSM8173840 r1,0:10 1:10 2:28 3:150,A:26800852330;C:18784742692;G:18161750085;T:20932990353;N:1857130,10,10,28,150,26800852330,18784742692,18161750085,20932990353,1857130,SRX24093154,SRS20882450,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31678,SRR28490923,SRX24093153,SRS20882449,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep2,GSM8173839,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep2,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173839,GSM8173839: zebrafish 14dpi rep2; Danio rerio; RNA Seq,GSM8173839 r1,GSM8173839,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19495X2 220201 A00421 0414 BH7MJYDSX3 S8 L004 I1 001.fastq.gz   read2PairFiles=19495X2 220201 A00421 0414 BH7MJYDSX3 S8 L004 I2 001.fastq.gz   read3PairFiles=19495X2 220201 A00421 0414 BH7MJYDSX3 S8 L004 R1 001.fastq.gz   read4PairFiles=19495X2 220201 A00421 0414 BH7MJYDSX3 S8 L004 R2 001.fastq.gz,19495X2_220201_A00421_0414_BH7MJYDSX3_S8_L004_I1_001.fastq.gz 19495X2_220201_A00421_0414_BH7MJYDSX3_S8_L004_I2_001.fastq.gz 19495X2_220201_A00421_0414_BH7MJYDSX3_S8_L004_R1_001.fastq.gz 19495X2_220201_A00421_0414_BH7MJYDSX3_S8_L004_R2_001.fastq.gz,fastq fastq fastq fastq,96751760292.0,488645254.0,GSM8173839 r1,0:10 1:10 2:28 3:150,A:26977933874;C:19374971991;G:18847897958;T:21776150237;N:1901152,10,10,28,150,26977933874,19374971991,18847897958,21776150237,1901152,SRX24093153,SRS20882449,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31679,SRR28490924,SRX24093152,SRS20882448,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 14dpi rep1,GSM8173838,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:14 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 14dpi rep1,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:14 xxx post injury,GSM8173838,GSM8173838: zebrafish 14dpi rep1; Danio rerio; RNA Seq,GSM8173838 r1,GSM8173838,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19495X1 220201 A00421 0414 BH7MJYDSX3 S7 L004 I1 001.fastq.gz   read2PairFiles=19495X1 220201 A00421 0414 BH7MJYDSX3 S7 L004 I2 001.fastq.gz   read3PairFiles=19495X1 220201 A00421 0414 BH7MJYDSX3 S7 L004 R1 001.fastq.gz   read4PairFiles=19495X1 220201 A00421 0414 BH7MJYDSX3 S7 L004 R2 001.fastq.gz,19495X1_220201_A00421_0414_BH7MJYDSX3_S7_L004_I1_001.fastq.gz 19495X1_220201_A00421_0414_BH7MJYDSX3_S7_L004_I2_001.fastq.gz 19495X1_220201_A00421_0414_BH7MJYDSX3_S7_L004_R1_001.fastq.gz 19495X1_220201_A00421_0414_BH7MJYDSX3_S7_L004_R2_001.fastq.gz,fastq fastq fastq fastq,90380046042.0,456464879.0,GSM8173838 r1,0:10 1:10 2:28 3:150,A:25630924753;C:18477012718;G:17083347155;T:20057683089;N:1780747,10,10,28,150,25630924753,18477012718,17083347155,20057683089,1780747,SRX24093152,SRS20882448,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31680,SRR28490925,SRX24093151,SRS20882447,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 3dpi rep3,GSM8173837,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:3 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 3dpi rep3,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:3 xxx post injury,GSM8173837,GSM8173837: zebrafish 3dpi rep3; Danio rerio; RNA Seq,GSM8173837 r1,GSM8173837,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 I1 001.fastq.gz   read2PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 I2 001.fastq.gz   read3PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 R1 001.fastq.gz   read4PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 R2 001.fastq.gz,19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_I1_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_I2_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_R1_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq,127733838606.0,645120397.0,GSM8173837 r1,0:10 1:10 2:28 3:150,A:33907907612;C:25406584124;G:25352400361;T:30160949616;N:3588953,10,10,28,150,33907907612,25406584124,25352400361,30160949616,3588953,SRX24093151,SRS20882447,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31681,SRR28490926,SRX24093150,SRS20882446,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 3dpi rep2,GSM8173836,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:3 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 3dpi rep2,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:3 xxx post injury,GSM8173836,GSM8173836: zebrafish 3dpi rep2; Danio rerio; RNA Seq,GSM8173836 r1,GSM8173836,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19630X5 220407 A00421 0430 AHL27JDSX3 S5 L004 I1 001.fastq.gz   read2PairFiles=19630X5 220407 A00421 0430 AHL27JDSX3 S5 L004 I2 001.fastq.gz   read3PairFiles=19630X5 220407 A00421 0430 AHL27JDSX3 S5 L004 R1 001.fastq.gz   read4PairFiles=19630X5 220407 A00421 0430 AHL27JDSX3 S5 L004 R2 001.fastq.gz,19630X5_220407_A00421_0430_AHL27JDSX3_S5_L004_I1_001.fastq.gz 19630X5_220407_A00421_0430_AHL27JDSX3_S5_L004_I2_001.fastq.gz 19630X5_220407_A00421_0430_AHL27JDSX3_S5_L004_R1_001.fastq.gz 19630X5_220407_A00421_0430_AHL27JDSX3_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq,88269296544.0,445804528.0,GSM8173836 r1,0:10 1:10 2:28 3:150,A:23691494771;C:17715287132;G:16934838063;T:21009112314;N:2473704,10,10,28,150,23691494771,17715287132,16934838063,21009112314,2473704,SRX24093150,SRS20882446,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31682,SRR28490927,SRX24093149,SRS20882445,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish 3dpi rep1,GSM8173835,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:3 xxx post injury|geo loc name:missing|collection date:missing,zebrafish 3dpi rep1,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:3 xxx post injury,GSM8173835,GSM8173835: zebrafish 3dpi rep1; Danio rerio; RNA Seq,GSM8173835 r1,GSM8173835,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19630X4 220407 A00421 0430 AHL27JDSX3 S4 L004 I1 001.fastq.gz   read2PairFiles=19630X4 220407 A00421 0430 AHL27JDSX3 S4 L004 I2 001.fastq.gz   read3PairFiles=19630X4 220407 A00421 0430 AHL27JDSX3 S4 L004 R1 001.fastq.gz   read4PairFiles=19630X4 220407 A00421 0430 AHL27JDSX3 S4 L004 R2 001.fastq.gz,19630X4_220407_A00421_0430_AHL27JDSX3_S4_L004_I1_001.fastq.gz 19630X4_220407_A00421_0430_AHL27JDSX3_S4_L004_I2_001.fastq.gz 19630X4_220407_A00421_0430_AHL27JDSX3_S4_L004_R1_001.fastq.gz 19630X4_220407_A00421_0430_AHL27JDSX3_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq,73276792776.0,370084812.0,GSM8173835 r1,0:10 1:10 2:28 3:150,A:19369278475;C:14629225553;G:14664402682;T:17210132889;N:2056937,10,10,28,150,19369278475,14629225553,14664402682,17210132889,2056937,SRX24093149,SRS20882445,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31683,SRR28490928,SRX24093148,SRS20882444,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish uninjured rep4,GSM8173834,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:Uninjured|geo loc name:missing|collection date:missing,zebrafish uninjured rep4,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:Uninjured,GSM8173834,GSM8173834: zebrafish uninjured rep4; Danio rerio; RNA Seq,GSM8173834 r1,GSM8173834,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19226X2 211001 A00421 0374 BHMGTFDSX2 S2 L004 I1 001.fastq.gz   read2PairFiles=19226X2 211001 A00421 0374 BHMGTFDSX2 S2 L004 I2 001.fastq.gz   read3PairFiles=19226X2 211001 A00421 0374 BHMGTFDSX2 S2 L004 R1 001.fastq.gz   read4PairFiles=19226X2 211001 A00421 0374 BHMGTFDSX2 S2 L004 R2 001.fastq.gz,19226X2_211001_A00421_0374_BHMGTFDSX2_S2_L004_I1_001.fastq.gz 19226X2_211001_A00421_0374_BHMGTFDSX2_S2_L004_I2_001.fastq.gz 19226X2_211001_A00421_0374_BHMGTFDSX2_S2_L004_R1_001.fastq.gz 19226X2_211001_A00421_0374_BHMGTFDSX2_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,88217468658.0,445542771.0,GSM8173834 r1,0:10 1:10 2:28 3:150,A:23594347570;C:18139448524;G:18958392712;T:18613143461;N:1280971,10,10,28,150,23594347570,18139448524,18958392712,18613143461,1280971,SRX24093148,SRS20882444,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31684,SRR28490929,SRX24093147,SRS20882443,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish uninjured rep3,GSM8173833,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:Uninjured|geo loc name:missing|collection date:missing,zebrafish uninjured rep3,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:Uninjured,GSM8173833,GSM8173833: zebrafish uninjured rep3; Danio rerio; RNA Seq,GSM8173833 r1,GSM8173833,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=19226X1 211001 A00421 0374 BHMGTFDSX2 S1 L004 I1 001.fastq.gz   read2PairFiles=19226X1 211001 A00421 0374 BHMGTFDSX2 S1 L004 I2 001.fastq.gz   read3PairFiles=19226X1 211001 A00421 0374 BHMGTFDSX2 S1 L004 R1 001.fastq.gz   read4PairFiles=19226X1 211001 A00421 0374 BHMGTFDSX2 S1 L004 R2 001.fastq.gz,19226X1_211001_A00421_0374_BHMGTFDSX2_S1_L004_I1_001.fastq.gz 19226X1_211001_A00421_0374_BHMGTFDSX2_S1_L004_I2_001.fastq.gz 19226X1_211001_A00421_0374_BHMGTFDSX2_S1_L004_R1_001.fastq.gz 19226X1_211001_A00421_0374_BHMGTFDSX2_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,74194991442.0,374722179.0,GSM8173833 r1,0:10 1:10 2:28 3:150,A:20240239572;C:15201039627;G:15390341020;T:15867858186;N:1069457,10,10,28,150,20240239572,15201039627,15390341020,15867858186,1069457,SRX24093147,SRS20882443,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31685,SRR28490930,SRX24093146,SRS20882442,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish uninjured rep2,GSM8173832,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:Uninjured|geo loc name:missing|collection date:missing,zebrafish uninjured rep2,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:Uninjured,GSM8173832,GSM8173832: zebrafish uninjured rep2; Danio rerio; RNA Seq,GSM8173832 r1,GSM8173832,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=18041X2 200623 A00421 0208 BHT77VDMXX S3 L001 I1 001.fastq.gz   read2PairFiles=18041X2 200623 A00421 0208 BHT77VDMXX S3 L001 R1 001.fastq.gz   read3PairFiles=18041X2 200623 A00421 0208 BHT77VDMXX S3 L001 R2 001.fastq.gz,18041X2_200623_A00421_0208_BHT77VDMXX_S3_L001_I1_001.fastq.gz 18041X2_200623_A00421_0208_BHT77VDMXX_S3_L001_R1_001.fastq.gz 18041X2_200623_A00421_0208_BHT77VDMXX_S3_L001_R2_001.fastq.gz,fastq fastq fastq,42126965160.0,226489060.0,GSM8173832 r1,0:8 1:28 2:150,A:11954731471;C:9381480553;G:8372128049;T:10605910330;N:802277,8,28,150,,11954731471,9381480553,8372128049,10605910330,802277,SRX24093146,SRS20882442,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
31686,SRR28490931,SRX24093145,SRS20882441,SRP498465,PRJNA1093008,Distinct features of the regenerating heart uncovered through comparative single cell profiling,GSE262689,Other,Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury,,,,zebrafish uninjured rep1,GSM8173831,,source name:Heart Ventricle|tissue:Heart Ventricle|treatment:Uninjured|geo loc name:missing|collection date:missing,zebrafish uninjured rep1,Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files,Heart Ventricle,Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,Wild type Tübingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.,tissue:Heart Ventricle|treatment:Uninjured,GSM8173831,GSM8173831: zebrafish uninjured rep1; Danio rerio; RNA Seq,GSM8173831 r1,GSM8173831,1,To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498465,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 I1 001.fastq.gz   read2PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 R1 001.fastq.gz   read3PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 R2 001.fastq.gz,18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_I1_001.fastq.gz 18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_R1_001.fastq.gz 18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_R2_001.fastq.gz,fastq fastq fastq,48849838812.0,262633542.0,GSM8173831 r1,0:8 1:28 2:150,A:13780412427;C:10982740007;G:9382145879;T:12602525920;N:946243,8,28,150,,13780412427,10982740007,9382145879,12602525920,946243,SRX24093145,SRS20882441,SRA1835934,"Gagnon, Biology, University of Utah","Gagnon, Biology, University of Utah",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-03-28,Adult,Adult,Heart,Cardiovascular System
32609,SRR29325925,SRX24842084,SRS21553259,SRP512516,PRJNA1121299,"Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study ""The heart is a niche for hematopoietic stem and progenitor cells in zebrafish.""",GSE269378,Transcriptome Analysis,We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study  we uncovered the presence of an endocardial hematopoietic cluster  along with other significant clusters including valve endocardial and interstitial cells  and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells  and further analyzed using scRNAseq.,,pubmed:39217144,,EC 2d,GSM8314110,,source name:Heart|tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:48 hpf loc name:missing|collection date:missing,EC 2d,Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore  we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs,Heart,,Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4·H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria™ III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.,Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf,tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:48 hpf,GSM8314110,GSM8314110: EC 2d; Danio rerio; RNA Seq,GSM8314110 r1,GSM8314110,1,Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4·H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria™ III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP512516,,,Felix_10x_Lib_EC-2d_R1.fastq.gz Felix_10x_Lib_EC-2d_R2.fastq.gz,fastq fastq,37849382027.0,476135961.0,GSM8314110 r1,0:28 1:51.49,A:10212120425;C:8162504214;G:8573129268;T:10704929378;N:196698742,28,51,,,10212120425,8162504214,8573129268,10704929378,196698742,SRX24842084,SRS21553259,SRA1892449,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2024-06-07,Hatching,Embryo,Heart,Cardiovascular System
32610,SRR29325926,SRX24842083,SRS21553258,SRP512516,PRJNA1121299,"Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study ""The heart is a niche for hematopoietic stem and progenitor cells in zebrafish.""",GSE269378,Transcriptome Analysis,We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study  we uncovered the presence of an endocardial hematopoietic cluster  along with other significant clusters including valve endocardial and interstitial cells  and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells  and further analyzed using scRNAseq.,,pubmed:39217144,,EC HC 3d,GSM8314111,,source name:Heart|tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:72 hpf loc name:missing|collection date:missing,EC HC 3d,Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore  we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs,Heart,,Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4·H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria™ III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.,Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf,tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:72 hpf,GSM8314111,GSM8314111: EC HC 3d; Danio rerio; RNA Seq,GSM8314111 r1,GSM8314111,1,Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4·H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria™ III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP512516,,,Felix_10x_Lib_EC-HC_3d_R1.fastq.gz Felix_10x_Lib_EC-HC_3d_R2.fastq.gz,fastq fastq,34745112542.0,437132766.0,GSM8314111 r1,0:28 1:51.48,A:9310358713;C:7641472951;G:8108829079;T:9501691105;N:182760694,28,51,,,9310358713,7641472951,8108829079,9501691105,182760694,SRX24842083,SRS21553258,SRA1892449,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2024-06-07,Larval,Larval,Heart,Cardiovascular System
33669,SRR30530658,SRX25954305,SRS22536191,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，high glucose,GSM8494124,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，high glucose,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494124,GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq,GSM8494124 r1,GSM8494124,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz,fastq fastq,196891371600.0,656304572.0,GSM8494124 r1,0:150 1:150,A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323,150,150,,,46034913013,37262343828,60636104680,52955473756,2536323,SRX25954305,SRS22536191,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33670,SRR30530659,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz,fastq fastq,18351420300.0,61171401.0,GSM8494123 r1,0:150 1:150,A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607,150,150,,,3872504772,3434009784,6583451920,4461384217,69607,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33671,SRR30530660,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz,fastq fastq,36386960400.0,121289868.0,GSM8494123 r2,0:150 1:150,A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278,150,150,,,8890006445,6974694151,10814990376,9707137150,132278,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33672,SRR30530661,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz,fastq fastq,44811813000.0,149372710.0,GSM8494123 r3,0:150 1:150,A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370,150,150,,,10939691275,8613307673,13332283843,11926366839,163370,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33673,SRR30530662,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz,fastq fastq,22587582300.0,75291941.0,GSM8494123 r4,0:150 1:150,A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737,150,150,,,4762937825,4235264474,8108549401,5480746863,83737,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33674,SRR30530663,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz,fastq fastq,31458502200.0,104861674.0,GSM8494123 r5,0:150 1:150,A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751,150,150,,,7597642424,6175910515,9377029875,8307805635,113751,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33675,SRR30530664,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz,fastq fastq,15812987400.0,52709958.0,GSM8494123 r6,0:150 1:150,A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817,150,150,,,3317721700,3009997461,5662825685,3822382737,59817,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33676,SRR30530665,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz,fastq fastq,19472976900.0,64909923.0,GSM8494123 r7,0:150 1:150,A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183,150,150,,,4109297307,3636046624,6996008921,4731548865,75183,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33677,SRR30530666,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz,fastq fastq,39005746200.0,130019154.0,GSM8494123 r8,0:150 1:150,A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785,150,150,,,9542890616,7456459618,11598648802,10407604379,142785,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
34072,SRR31040127,SRX26425404,SRS22944868,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L004,GSM8581895,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581895,GSM8581895: Cited UI L004; Danio rerio; RNA Seq,GSM8581895 r1,GSM8581895,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8751034986.0,63413297.0,GSM8581895 r1,0:28 1:90 2:10 3:10,A:1848966031;C:1012706988;G:1157260676;T:1688231038;N:31997,28,90,10,10,1848966031,1012706988,1157260676,1688231038,31997,SRX26425404,SRS22944868,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34073,SRR31040128,SRX26425403,SRS22944867,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L003,GSM8581894,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581894,GSM8581894: Cited UI L003; Danio rerio; RNA Seq,GSM8581894 r1,GSM8581894,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8965044420.0,64964090.0,GSM8581894 r1,0:28 1:90 2:10 3:10,A:1889187704;C:1042838950;G:1192357586;T:1722353910;N:29950,28,90,10,10,1889187704,1042838950,1192357586,1722353910,29950,SRX26425403,SRS22944867,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34074,SRR31040129,SRX26425402,SRS22944866,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L002,GSM8581893,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581893,GSM8581893: Cited UI L002; Danio rerio; RNA Seq,GSM8581893 r1,GSM8581893,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9234521850.0,66916825.0,GSM8581893 r1,0:28 1:90 2:10 3:10,A:1942032508;C:1074923961;G:1229240783;T:1776284178;N:32820,28,90,10,10,1942032508,1074923961,1229240783,1776284178,32820,SRX26425402,SRS22944866,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34075,SRR31040130,SRX26425401,SRS22944865,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L001,GSM8581892,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581892,GSM8581892: Cited UI L001; Danio rerio; RNA Seq,GSM8581892 r1,GSM8581892,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9307917288.0,67448676.0,GSM8581892 r1,0:28 1:90 2:10 3:10,A:1956920944;C:1083084138;G:1238610324;T:1791739835;N:25599,28,90,10,10,1956920944,1083084138,1238610324,1791739835,25599,SRX26425401,SRS22944865,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34076,SRR31040131,SRX26425400,SRS22944864,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L004,GSM8581891,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581891,GSM8581891: Cited 3dpa L004; Danio rerio; RNA Seq,GSM8581891 r1,GSM8581891,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq,7170951684.0,51963418.0,GSM8581891 r1,0:28 1:90 2:10 3:10,A:1540735099;C:805699399;G:919379467;T:1410866922;N:26733,28,90,10,10,1540735099,805699399,919379467,1410866922,26733,SRX26425400,SRS22944864,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34077,SRR31040132,SRX26425399,SRS22944863,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L003,GSM8581890,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581890,GSM8581890: Cited 3dpa L003; Danio rerio; RNA Seq,GSM8581890 r1,GSM8581890,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R2_001.fastq.gz,fastq fastq fastq fastq,7291420716.0,52836382.0,GSM8581890 r1,0:28 1:90 2:10 3:10,A:1561481957;C:822744414;G:938546253;T:1432477210;N:24546,28,90,10,10,1561481957,822744414,938546253,1432477210,24546,SRX26425399,SRS22944863,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34078,SRR31040133,SRX26425398,SRS22944862,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L002,GSM8581889,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581889,GSM8581889: Cited 3dpa L002; Danio rerio; RNA Seq,GSM8581889 r1,GSM8581889,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,7477578162.0,54185349.0,GSM8581889 r1,0:28 1:90 2:10 3:10,A:1599788142;C:843874544;G:963283854;T:1469708656;N:26214,28,90,10,10,1599788142,843874544,963283854,1469708656,26214,SRX26425398,SRS22944862,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34079,SRR31040134,SRX26425397,SRS22944861,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L001,GSM8581888,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581888,GSM8581888: Cited 3dpa L001; Danio rerio; RNA Seq,GSM8581888 r1,GSM8581888,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,7511701146.0,54432617.0,GSM8581888 r1,0:28 1:90 2:10 3:10,A:1606850913;C:847555151;G:967521409;T:1476987489;N:20568,28,90,10,10,1606850913,847555151,967521409,1476987489,20568,SRX26425397,SRS22944861,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34080,SRR31040135,SRX26425396,SRS22944860,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L004,GSM8581887,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581887,GSM8581887: WT UI L004; Danio rerio; RNA Seq,GSM8581887 r1,GSM8581887,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8744622816.0,63366832.0,GSM8581887 r1,0:28 1:90 2:10 3:10,A:1804235390;C:1112990195;G:1270205014;T:1515005620;N:578661,28,90,10,10,1804235390,1112990195,1270205014,1515005620,578661,SRX26425396,SRS22944860,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34081,SRR31040136,SRX26425395,SRS22944859,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L003,GSM8581886,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581886,GSM8581886: WT UI L003; Danio rerio; RNA Seq,GSM8581886 r1,GSM8581886,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8629549722.0,62532969.0,GSM8581886 r1,0:28 1:90 2:10 3:10,A:1780671193;C:1097605584;G:1253098096;T:1495999781;N:592556,28,90,10,10,1780671193,1097605584,1253098096,1495999781,592556,SRX26425395,SRS22944859,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34082,SRR31040137,SRX26425394,SRS22944858,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L002,GSM8581885,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581885,GSM8581885: WT UI L002; Danio rerio; RNA Seq,GSM8581885 r1,GSM8581885,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8810036748.0,63840846.0,GSM8581885 r1,0:28 1:90 2:10 3:10,A:1816298911;C:1122594552;G:1280394245;T:1525799551;N:588881,28,90,10,10,1816298911,1122594552,1280394245,1525799551,588881,SRX26425394,SRS22944858,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34083,SRR31040138,SRX26425393,SRS22944857,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L001,GSM8581884,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581884,GSM8581884: WT UI L001; Danio rerio; RNA Seq,GSM8581884 r1,GSM8581884,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8890601838.0,64424651.0,GSM8581884 r1,0:28 1:90 2:10 3:10,A:1831803855;C:1133337909;G:1293064278;T:1539489836;N:522712,28,90,10,10,1831803855,1133337909,1293064278,1539489836,522712,SRX26425393,SRS22944857,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34084,SRR31040139,SRX26425392,SRS22944856,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L004,GSM8581883,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581883,GSM8581883: WT 3dpa L004; Danio rerio; RNA Seq,GSM8581883 r1,GSM8581883,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq,10259680380.0,74345510.0,GSM8581883 r1,0:28 1:90 2:10 3:10,A:2030501498;C:1372342288;G:1610608028;T:1676971327;N:672759,28,90,10,10,2030501498,1372342288,1610608028,1676971327,672759,SRX26425392,SRS22944856,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34085,SRR31040140,SRX26425391,SRS22944855,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L003,GSM8581882,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581882,GSM8581882: WT 3dpa L003; Danio rerio; RNA Seq,GSM8581882 r1,GSM8581882,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10153022940.0,73572630.0,GSM8581882 r1,0:28 1:90 2:10 3:10,A:2010560616;C:1356907781;G:1592695197;T:1660694697;N:678409,28,90,10,10,2010560616,1356907781,1592695197,1660694697,678409,SRX26425391,SRS22944855,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34086,SRR31040141,SRX26425390,SRS22944854,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L002,GSM8581881,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581881,GSM8581881: WT 3dpa L002; Danio rerio; RNA Seq,GSM8581881 r1,GSM8581881,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10374062784.0,75174368.0,GSM8581881 r1,0:28 1:90 2:10 3:10,A:2050663376;C:1389631407;G:1629809936;T:1694915558;N:672843,28,90,10,10,2050663376,1389631407,1629809936,1694915558,672843,SRX26425390,SRS22944854,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34087,SRR31040142,SRX26425389,SRS22944853,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L001,GSM8581880,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581880,GSM8581880: WT 3dpa L001; Danio rerio; RNA Seq,GSM8581880 r1,GSM8581880,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,10577377770.0,76647665.0,GSM8581880 r1,0:28 1:90 2:10 3:10,A:2089361892;C:1417156705;G:1662751139;T:1728402830;N:617284,28,90,10,10,2089361892,1417156705,1662751139,1728402830,617284,SRX26425389,SRS22944853,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
51190,SRR8592250,SRX5392462,SRS4380285,SRP186305,PRJNA522917,Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation,GSE126647,Transcriptome Analysis,Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated  few signals are understood that specifically restrict the size of the vertebrate OFT. Here  we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants  which lack the transcription factor Pbx4  produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically  optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors  which contribute to the OFT  and adjacent endothelial cell progenitors  which contribute to posterior pharyngeal arch arteries. Subsequently  Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior  differentiated cardiomyocyte populations. Therefore  the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes  we utilized  single cell RNA Seq scRNA Seq data sets collected from  control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.,,pubmed:32094112,,Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq,GSM3610371,,source name:Pbx4 depleted nkx2.5:ZsYellow+ cells|strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells,Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq,Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment  filtering  barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv  Genes genes.tsv  and Matrix matrix.mtx,Pbx4 depleted nkx2.5:ZsYellow+ cells,,Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5°C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry,,strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells,GSM3610371,GSM3610371: Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq,GSM3610371,,1,Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5°C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry,GEO Accession:GSM3610371,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP186305,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10X PBX4 mo injected 3zf S2 L001 I1 001.fastq.gz   read2PairFiles=10X PBX4 mo injected 3zf S2 L001 R1 001.fastq.gz   read3PairFiles=10X PBX4 mo injected 3zf S2 L001 R2 001.fastq.gz,10X_PBX4_mo_injected_3zf_S2_L001_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R2_001.fastq.gz,fastq fastq fastq,13771731610.0,75668855.0,GSM3610371 r1,0:8 1:27 2:147,A:3868981340;C:3004344480;G:3173242889;T:3705905113;N:19257788,8,27,147,,3868981340,3004344480,3173242889,3705905113,19257788,SRX5392462,SRS4380285,SRA850447,GEO,"Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital",1,0.91532,,0.07049,,0.82722,,0.50962,,147,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-02-15,Pharyngula,Embryo,Heart,Cardiovascular System
51191,SRR8592251,SRX5392462,SRS4380285,SRP186305,PRJNA522917,Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation,GSE126647,Transcriptome Analysis,Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated  few signals are understood that specifically restrict the size of the vertebrate OFT. Here  we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants  which lack the transcription factor Pbx4  produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically  optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors  which contribute to the OFT  and adjacent endothelial cell progenitors  which contribute to posterior pharyngeal arch arteries. Subsequently  Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior  differentiated cardiomyocyte populations. Therefore  the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes  we utilized  single cell RNA Seq scRNA Seq data sets collected from  control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.,,pubmed:32094112,,Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq,GSM3610371,,source name:Pbx4 depleted nkx2.5:ZsYellow+ cells|strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells,Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq,Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment  filtering  barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv  Genes genes.tsv  and Matrix matrix.mtx,Pbx4 depleted nkx2.5:ZsYellow+ cells,,Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5°C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry,,strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells,GSM3610371,GSM3610371: Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq,GSM3610371,,1,Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5°C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry,GEO Accession:GSM3610371,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP186305,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10X PBX4 mo injected 3zf S2 L002 I1 001.fastq.gz   read2PairFiles=10X PBX4 mo injected 3zf S2 L002 R1 001.fastq.gz   read3PairFiles=10X PBX4 mo injected 3zf S2 L002 R2 001.fastq.gz,10X_PBX4_mo_injected_3zf_S2_L002_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R2_001.fastq.gz,fastq fastq fastq,13960104704.0,76703872.0,GSM3610371 r2,0:8 1:27 2:147,A:3921736827;C:3045954411;G:3216708567;T:3758217760;N:17487139,8,27,147,,3921736827,3045954411,3216708567,3758217760,17487139,SRX5392462,SRS4380285,SRA850447,GEO,"Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital",1,0.91469,,0.06915,,0.82747,,0.49959,,147,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-02-15,Pharyngula,Embryo,Heart,Cardiovascular System
55246,SRR10203908,SRX6923953,SRS5454835,SRP223736,PRJNA575000,­runx1 controls zebrafish heart regeneration by promoting scar deposition as well as inhibiting myocardial proliferation and survival,GSE138181,Transcriptome Analysis,Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types  during both development and maturity. Here  we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration  but unexpectedly  absence of runx1 results in enhanced regeneration. Using single cell sequencing  we found that the wild type injury site consists of Runx1 positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without xxx into myofibroblasts. Both these populations are absent in runx1 mutants  resulting in a less collagenous and fibrinous scar. The reduction in fibrin in the mutant is further explained by reduced myofibroblast formation and by upregulation of components of the fibrin degradation pathway  including plasminogen receptor Annexin 2A as well as downregulation of plasminogen activator inhibitor serpine1 in myocardium and endocardium  resulting in increased levels of Plasminogen. In addition  this we also find enhanced myocardial proliferation as well as increased myocardial survival in the mutant. Our findings suggest that Runx1 controls the regenerative response of multiple cardiac cell types and that targeting Runx1 is a novel therapeutic strategy to induce endogenous heart repair. Overall design: To determine the differences between wild type  wild type injured and wild type runx1 KO runx1+ endothelial cells in Zebrafish,,pubmed:32341028,,587680 47,GSM4101382,,source name:Injured runx1 KO|tissue:Heart Ventricle pool 20 hearts|strain:KCL|genotype:runx1 KO|treatment:injured,587680 47,Reads aligned to Danio rerio.GRCz11 release 94 and processed using Cell Ranger v2.1.1 Counts extracted using scanpy in python Genome build: Danio rerio.GRCz11 release 94 Supplementary files format and content: Counts: Mapped read counts per gene  per cell,Injured runx1 KO,A small incision was made through the thorax and the pericardium using forceps and spring scissors. The abdomen was gently squeezed to expose the ventricle and tissue paper was used to dry the heart. A cryo probe with a copper filament was cooled in liquid nitrogen and placed on the ventricle surface until thawing was observed. Body wall incisions were not sutured  and post surgery  fish were returned to water and stimulated to breathe by pipetting water over the gills until the fish started swimming again. For sham surgery  the thorax and pericardial sac were opened  but the heart was not injured. All operated fish were kept in individual tanks for the first week post surgery  then fish were combined in larger tanks.,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,Adult wild type wt KCL strain  Tgkdrl:Hsa.HRAS mCherry34 subsequently referred to as Tgkdrl:mCherry and runx1W84X mutants27  TgBACrunx1P2:Citrine29  were housed in a Techniplast aquarium system [28 °C  14/10 hours light/dark cycle  fed 3x daily with dry food and brine shrimp]. All double transgenic lines on wild type or mutant background were generated by natural mating.,tissue:Heart Ventricle  pool 20 hearts|strain:KCL|genotype:runx1 KO|treatment:injured,GSM4101382,GSM4101382: 587680 47; Danio rerio; RNA Seq,GSM4101382,,1,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,GEO Accession:GSM4101382,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223736,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=587680 47 S62 L005 I1 001.fastq.gz   read2PairFiles=587680 47 S62 L005 R1 001.fastq.gz   read3PairFiles=587680 47 S62 L005 R2 001.fastq.gz,587680_47_S62_L005_I1_001.fastq.gz 587680_47_S62_L005_R1_001.fastq.gz 587680_47_S62_L005_R2_001.fastq.gz,fastq fastq fastq,10467709560.0,79300830.0,GSM4101382 r1,0:8 1:26 2:98,A:2859438039;C:2396178995;G:2404795699;T:2802486902;N:4809925,8,26,98,,2859438039,2396178995,2404795699,2802486902,4809925,SRX6923953,SRS5454835,SRA969982,GEO,"Haematology, University of Cambridge",1,0.89929,,0.09034,,0.8505,,0.53912,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2019-09-30,Adult,Adult,Heart,Cardiovascular System
55247,SRR10203907,SRX6923952,SRS5454834,SRP223736,PRJNA575000,­runx1 controls zebrafish heart regeneration by promoting scar deposition as well as inhibiting myocardial proliferation and survival,GSE138181,Transcriptome Analysis,Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types  during both development and maturity. Here  we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration  but unexpectedly  absence of runx1 results in enhanced regeneration. Using single cell sequencing  we found that the wild type injury site consists of Runx1 positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without xxx into myofibroblasts. Both these populations are absent in runx1 mutants  resulting in a less collagenous and fibrinous scar. The reduction in fibrin in the mutant is further explained by reduced myofibroblast formation and by upregulation of components of the fibrin degradation pathway  including plasminogen receptor Annexin 2A as well as downregulation of plasminogen activator inhibitor serpine1 in myocardium and endocardium  resulting in increased levels of Plasminogen. In addition  this we also find enhanced myocardial proliferation as well as increased myocardial survival in the mutant. Our findings suggest that Runx1 controls the regenerative response of multiple cardiac cell types and that targeting Runx1 is a novel therapeutic strategy to induce endogenous heart repair. Overall design: To determine the differences between wild type  wild type injured and wild type runx1 KO runx1+ endothelial cells in Zebrafish,,pubmed:32341028,,587680 46,GSM4101381,,source name:Injured Wild Type|tissue:Heart Ventricle pool 20 hearts|strain:KCL|genotype:WT|treatment:injured,587680 46,Reads aligned to Danio rerio.GRCz11 release 94 and processed using Cell Ranger v2.1.1 Counts extracted using scanpy in python Genome build: Danio rerio.GRCz11 release 94 Supplementary files format and content: Counts: Mapped read counts per gene  per cell,Injured Wild Type,A small incision was made through the thorax and the pericardium using forceps and spring scissors. The abdomen was gently squeezed to expose the ventricle and tissue paper was used to dry the heart. A cryo probe with a copper filament was cooled in liquid nitrogen and placed on the ventricle surface until thawing was observed. Body wall incisions were not sutured  and post surgery  fish were returned to water and stimulated to breathe by pipetting water over the gills until the fish started swimming again. For sham surgery  the thorax and pericardial sac were opened  but the heart was not injured. All operated fish were kept in individual tanks for the first week post surgery  then fish were combined in larger tanks.,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,Adult wild type wt KCL strain  Tgkdrl:Hsa.HRAS mCherry34 subsequently referred to as Tgkdrl:mCherry and runx1W84X mutants27  TgBACrunx1P2:Citrine29  were housed in a Techniplast aquarium system [28 °C  14/10 hours light/dark cycle  fed 3x daily with dry food and brine shrimp]. All double transgenic lines on wild type or mutant background were generated by natural mating.,tissue:Heart Ventricle  pool 20 hearts|strain:KCL|genotype:WT|treatment:injured,GSM4101381,GSM4101381: 587680 46; Danio rerio; RNA Seq,GSM4101381,,1,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,GEO Accession:GSM4101381,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223736,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=587680 46 S61 L005 I1 001.fastq.gz   read2PairFiles=587680 46 S61 L005 R1 001.fastq.gz   read3PairFiles=587680 46 S61 L005 R2 001.fastq.gz,587680_46_S61_L005_R2_001.fastq.gz 587680_46_S61_L005_R1_001.fastq.gz 587680_46_S61_L005_I1_001.fastq.gz,fastq fastq fastq,11549206680.0,87493990.0,GSM4101381 r1,0:8 1:26 2:98,A:3276822567;C:2531188698;G:2569553917;T:3166325098;N:5316400,8,26,98,,3276822567,2531188698,2569553917,3166325098,5316400,SRX6923952,SRS5454834,SRA969982,GEO,"Haematology, University of Cambridge",1,0.91155,,0.11038,,0.84143,,0.5481,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2019-09-30,Adult,Adult,Heart,Cardiovascular System
55248,SRR10203906,SRX6923951,SRS5454833,SRP223736,PRJNA575000,­runx1 controls zebrafish heart regeneration by promoting scar deposition as well as inhibiting myocardial proliferation and survival,GSE138181,Transcriptome Analysis,Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types  during both development and maturity. Here  we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration  but unexpectedly  absence of runx1 results in enhanced regeneration. Using single cell sequencing  we found that the wild type injury site consists of Runx1 positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without xxx into myofibroblasts. Both these populations are absent in runx1 mutants  resulting in a less collagenous and fibrinous scar. The reduction in fibrin in the mutant is further explained by reduced myofibroblast formation and by upregulation of components of the fibrin degradation pathway  including plasminogen receptor Annexin 2A as well as downregulation of plasminogen activator inhibitor serpine1 in myocardium and endocardium  resulting in increased levels of Plasminogen. In addition  this we also find enhanced myocardial proliferation as well as increased myocardial survival in the mutant. Our findings suggest that Runx1 controls the regenerative response of multiple cardiac cell types and that targeting Runx1 is a novel therapeutic strategy to induce endogenous heart repair. Overall design: To determine the differences between wild type  wild type injured and wild type runx1 KO runx1+ endothelial cells in Zebrafish,,pubmed:32341028,,587680 45,GSM4101380,,source name:Uninjured Wild Type|tissue:Heart Ventricle pool 20 hearts|strain:KCL|genotype:WT|treatment:uninjured,587680 45,Reads aligned to Danio rerio.GRCz11 release 94 and processed using Cell Ranger v2.1.1 Counts extracted using scanpy in python Genome build: Danio rerio.GRCz11 release 94 Supplementary files format and content: Counts: Mapped read counts per gene  per cell,Uninjured Wild Type,A small incision was made through the thorax and the pericardium using forceps and spring scissors. The abdomen was gently squeezed to expose the ventricle and tissue paper was used to dry the heart. A cryo probe with a copper filament was cooled in liquid nitrogen and placed on the ventricle surface until thawing was observed. Body wall incisions were not sutured  and post surgery  fish were returned to water and stimulated to breathe by pipetting water over the gills until the fish started swimming again. For sham surgery  the thorax and pericardial sac were opened  but the heart was not injured. All operated fish were kept in individual tanks for the first week post surgery  then fish were combined in larger tanks.,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,Adult wild type wt KCL strain  Tgkdrl:Hsa.HRAS mCherry34 subsequently referred to as Tgkdrl:mCherry and runx1W84X mutants27  TgBACrunx1P2:Citrine29  were housed in a Techniplast aquarium system [28 °C  14/10 hours light/dark cycle  fed 3x daily with dry food and brine shrimp]. All double transgenic lines on wild type or mutant background were generated by natural mating.,tissue:Heart Ventricle  pool 20 hearts|strain:KCL|genotype:WT|treatment:uninjured,GSM4101380,GSM4101380: 587680 45; Danio rerio; RNA Seq,GSM4101380,,1,Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65°C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.,GEO Accession:GSM4101380,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223736,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=587680 45 S60 L005 I1 001.fastq.gz   read2PairFiles=587680 45 S60 L005 R1 001.fastq.gz   read3PairFiles=587680 45 S60 L005 R2 001.fastq.gz,587680_45_S60_L005_I1_001.fastq.gz 587680_45_S60_L005_R1_001.fastq.gz 587680_45_S60_L005_R2_001.fastq.gz,fastq fastq fastq,11134774992.0,84354356.0,GSM4101380 r1,0:8 1:26 2:98,A:3152110963;C:2379819000;G:2458427917;T:3139288192;N:5128920,8,26,98,,3152110963,2379819000,2458427917,3139288192,5128920,SRX6923951,SRS5454833,SRA969982,GEO,"Haematology, University of Cambridge",1,0.90136,,0.13254,,0.84593,,0.51719,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2019-09-30,Adult,Adult,Heart,Cardiovascular System
56283,SRR10899959,SRX7568764,SRS6004889,SRP242096,PRJNA601476,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE143750,Transcriptome Analysis,An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly  a cell population with a skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Overall design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single cell RNA seq,,,,10X Etv2 homozygous 20ss,GSM4273675,,tissue:FACS sorted GFP+ endothelial cells|age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous,10X Etv2 homozygous 20ss,All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.9  and to obtain the gene expression matrices Genome build: GRCz10 Supplementary files format and content: mtx matrix files,FACS sorted GFP+ endothelial cells,,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,,age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous,GSM4273675,GSM4273675: 10X Etv2 homozygous 20ss; Danio rerio; RNA Seq,GSM4273675,,1,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,GEO Accession:GSM4273675,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP242096,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=10X Homo S1 L001 I1 001.fastq.gz   read2PairFiles=10X Homo S1 L001 R1 001.fastq.gz   read3PairFiles=10X Homo S1 L001 R2 001.fastq.gz,10X_Homo_S1_L001_R2_001.fastq.gz 10X_Homo_S1_L001_R1_001.fastq.gz 10X_Homo_S1_L001_I1_001.fastq.gz,fastq fastq fastq,14265440280.0,78381540.0,GSM4273675 r1,0:8 1:27 2:147,A:4380181360;C:2963120216;G:3162327779;T:3757758592;N:2052333,8,27,147,,4380181360,2963120216,3162327779,3757758592,2052333,SRX7568764,SRS6004889,SRA1026915,GEO,Cincinnati Children's Hospital,1,0.85534,,0.08164,,0.8504,,0.47433,,147,,B,,usable mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2020-01-15,Segmentation,Embryo,Endothelium,Cardiovascular System
56284,SRR10899960,SRX7568764,SRS6004889,SRP242096,PRJNA601476,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE143750,Transcriptome Analysis,An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly  a cell population with a skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Overall design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single cell RNA seq,,,,10X Etv2 homozygous 20ss,GSM4273675,,tissue:FACS sorted GFP+ endothelial cells|age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous,10X Etv2 homozygous 20ss,All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.9  and to obtain the gene expression matrices Genome build: GRCz10 Supplementary files format and content: mtx matrix files,FACS sorted GFP+ endothelial cells,,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,,age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous,GSM4273675,GSM4273675: 10X Etv2 homozygous 20ss; Danio rerio; RNA Seq,GSM4273675,,1,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,GEO Accession:GSM4273675,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP242096,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=10X Homo S1 L002 I1 001.fastq.gz   read2PairFiles=10X Homo S1 L002 R1 001.fastq.gz   read3PairFiles=10X Homo S1 L002 R2 001.fastq.gz,10X_Homo_S1_L002_R2_001.fastq.gz 10X_Homo_S1_L002_R1_001.fastq.gz 10X_Homo_S1_L002_I1_001.fastq.gz,fastq fastq fastq,14672202090.0,80616495.0,GSM4273675 r2,0:8 1:27 2:147,A:4504330378;C:3047430997;G:3252225360;T:3865730356;N:2484999,8,27,147,,4504330378,3047430997,3252225360,3865730356,2484999,SRX7568764,SRS6004889,SRA1026915,GEO,Cincinnati Children's Hospital,1,0.85397,,0.08065,,0.85362,,0.47925,,147,,B,,usable mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2020-01-15,Segmentation,Embryo,Endothelium,Cardiovascular System
56285,SRR10899957,SRX7568763,SRS6004888,SRP242096,PRJNA601476,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE143750,Transcriptome Analysis,An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly  a cell population with a skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Overall design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single cell RNA seq,,,,10X Etv2 heterozygous 20ss,GSM4273674,,tissue:FACS sorted GFP+ endothelial cells|age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 heterozygous,10X Etv2 heterozygous 20ss,All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.9  and to obtain the gene expression matrices Genome build: GRCz10 Supplementary files format and content: mtx matrix files,FACS sorted GFP+ endothelial cells,,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,,age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 heterozygous,GSM4273674,GSM4273674: 10X Etv2 heterozygous 20ss; Danio rerio; RNA Seq,GSM4273674,,1,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,GEO Accession:GSM4273674,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP242096,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=10X Het S2 L001 I1 001.fastq.gz   read2PairFiles=10X Het S2 L001 R1 001.fastq.gz   read3PairFiles=10X Het S2 L001 R2 001.fastq.gz,10X_Het_S2_L001_R2_001.fastq.gz 10X_Het_S2_L001_R1_001.fastq.gz 10X_Het_S2_L001_I1_001.fastq.gz,fastq fastq fastq,16028775854.0,88070197.0,GSM4273674 r1,0:8 1:27 2:147,A:4841927214;C:3312520117;G:3546106776;T:4325878552;N:2343195,8,27,147,,4841927214,3312520117,3546106776,4325878552,2343195,SRX7568763,SRS6004888,SRA1026915,GEO,Cincinnati Children's Hospital,1,0.85679,,0.0914,,0.84423,,0.50119,,147,,B,,usable mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2020-01-15,Segmentation,Embryo,Endothelium,Cardiovascular System
56286,SRR10899958,SRX7568763,SRS6004888,SRP242096,PRJNA601476,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE143750,Transcriptome Analysis,An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly  a cell population with a skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Overall design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single cell RNA seq,,,,10X Etv2 heterozygous 20ss,GSM4273674,,tissue:FACS sorted GFP+ endothelial cells|age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 heterozygous,10X Etv2 heterozygous 20ss,All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.9  and to obtain the gene expression matrices Genome build: GRCz10 Supplementary files format and content: mtx matrix files,FACS sorted GFP+ endothelial cells,,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,,age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 heterozygous,GSM4273674,GSM4273674: 10X Etv2 heterozygous 20ss; Danio rerio; RNA Seq,GSM4273674,,1,Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted  and amplified by PCR  and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol,GEO Accession:GSM4273674,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP242096,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=10X Het S2 L002 I1 001.fastq.gz   read2PairFiles=10X Het S2 L002 R1 001.fastq.gz   read3PairFiles=10X Het S2 L002 R2 001.fastq.gz,10X_Het_S2_L002_I1_001.fastq.gz 10X_Het_S2_L002_R1_001.fastq.gz 10X_Het_S2_L002_R2_001.fastq.gz,fastq fastq fastq,16500118362.0,90659991.0,GSM4273674 r2,0:8 1:27 2:147,A:4982587485;C:3409998223;G:3650593667;T:4454135325;N:2803662,8,27,147,,4982587485,3409998223,3650593667,4454135325,2803662,SRX7568763,SRS6004888,SRA1026915,GEO,Cincinnati Children's Hospital,1,0.85659,,0.09023,,0.84567,,0.51573,,147,,B,,usable mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2020-01-15,Segmentation,Embryo,Endothelium,Cardiovascular System
56905,SRR11186480,SRX7806775,SRS6219810,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 2,GSM4340650,,source name:kit 14dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 14dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340650,GSM4340650: kit 14dpi 2; Danio rerio; RNA Seq,GSM4340650,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340650,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 2 S1 L001 I1 001.fastq.gz   read2PairFiles=kit 14dpi 2 S1 L001 R2 001.fastq.gz   read3PairFiles=kit 14dpi 2 S1 L001 R1 001.fastq.gz,kit_14dpi_2_S1_L001_I1_001.fastq.gz kit_14dpi_2_S1_L001_R1_001.fastq.gz kit_14dpi_2_S1_L001_R2_001.fastq.gz,fastq fastq fastq,7781791908.0,58952969.0,GSM4340650 r1,0:8 1:98 2:26,A:2242466212;C:1778372877;G:1667223932;T:2089876413;N:3852474,8,98,26,,2242466212,1778372877,1667223932,2089876413,3852474,SRX7806775,SRS6219810,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94352,0.00297,0.08008,0.00074,0.88779,0.99577,0.84163,0.52098,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56906,SRR11186481,SRX7806775,SRS6219810,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 2,GSM4340650,,source name:kit 14dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 14dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340650,GSM4340650: kit 14dpi 2; Danio rerio; RNA Seq,GSM4340650,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340650,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 2 S1 L002 I1 001.fastq.gz   read2PairFiles=kit 14dpi 2 S1 L002 R2 001.fastq.gz   read3PairFiles=kit 14dpi 2 S1 L002 R1 001.fastq.gz,kit_14dpi_2_S1_L002_I1_001.fastq.gz kit_14dpi_2_S1_L002_R1_001.fastq.gz kit_14dpi_2_S1_L002_R2_001.fastq.gz,fastq fastq fastq,7680504876.0,58185643.0,GSM4340650 r2,0:8 1:98 2:26,A:2215552067;C:1754278212;G:1645737729;T:2061243503;N:3693365,8,98,26,,2215552067,1754278212,1645737729,2061243503,3693365,SRX7806775,SRS6219810,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94281,0.00306,0.08095,0.0007,0.88797,0.99539,0.83857,0.53023,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56907,SRR11186482,SRX7806775,SRS6219810,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 2,GSM4340650,,source name:kit 14dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 14dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340650,GSM4340650: kit 14dpi 2; Danio rerio; RNA Seq,GSM4340650,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340650,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 2 S1 L003 I1 001.fastq.gz   read2PairFiles=kit 14dpi 2 S1 L003 R2 001.fastq.gz   read3PairFiles=kit 14dpi 2 S1 L003 R1 001.fastq.gz,kit_14dpi_2_S1_L003_I1_001.fastq.gz kit_14dpi_2_S1_L003_R1_001.fastq.gz kit_14dpi_2_S1_L003_R2_001.fastq.gz,fastq fastq fastq,7725611256.0,58527358.0,GSM4340650 r3,0:8 1:98 2:26,A:2228852971;C:1768011504;G:1653774472;T:2074726261;N:246048,8,98,26,,2228852971,1768011504,1653774472,2074726261,246048,SRX7806775,SRS6219810,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94385,0.00316,0.08148,0.00075,0.88789,0.99494,0.83718,0.48409,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56908,SRR11186483,SRX7806775,SRS6219810,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 2,GSM4340650,,source name:kit 14dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 14dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340650,GSM4340650: kit 14dpi 2; Danio rerio; RNA Seq,GSM4340650,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340650,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 2 S1 L004 I1 001.fastq.gz   read2PairFiles=kit 14dpi 2 S1 L004 R2 001.fastq.gz   read3PairFiles=kit 14dpi 2 S1 L004 R1 001.fastq.gz,kit_14dpi_2_S1_L004_I1_001.fastq.gz kit_14dpi_2_S1_L004_R1_001.fastq.gz kit_14dpi_2_S1_L004_R2_001.fastq.gz,fastq fastq fastq,7609286784.0,57646112.0,GSM4340650 r4,0:8 1:98 2:26,A:2193739560;C:1740109633;G:1632147594;T:2042974222;N:315775,8,98,26,,2193739560,1740109633,1632147594,2042974222,315775,SRX7806775,SRS6219810,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94258,0.00309,0.08184,0.00073,0.89016,0.99527,0.84133,0.51415,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56909,SRR11186476,SRX7806774,SRS6219809,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 1,GSM4340649,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340649,GSM4340649: kit 14dpi 1; Danio rerio; RNA Seq,GSM4340649,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340649,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 1 S1 L001 I1 001.fastq.gz   read2PairFiles=kit 14dpi 1 S1 L001 R2 001.fastq.gz   read3PairFiles=kit 14dpi 1 S1 L001 R1 001.fastq.gz,kit_14dpi_1_S1_L001_I1_001.fastq.gz kit_14dpi_1_S1_L001_R1_001.fastq.gz kit_14dpi_1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,7722224136.0,58501698.0,GSM4340649 r1,0:8 1:98 2:26,A:2225663837;C:1761078052;G:1766349345;T:1968017965;N:1114937,8,98,26,,2225663837,1761078052,1766349345,1968017965,1114937,SRX7806774,SRS6219809,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94765,0.00393,0.05485,0.0007,0.8801,0.99421,0.66266,0.57166,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56910,SRR11186477,SRX7806774,SRS6219809,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 1,GSM4340649,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340649,GSM4340649: kit 14dpi 1; Danio rerio; RNA Seq,GSM4340649,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340649,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 1 S1 L002 I1 001.fastq.gz   read2PairFiles=kit 14dpi 1 S1 L002 R2 001.fastq.gz   read3PairFiles=kit 14dpi 1 S1 L002 R1 001.fastq.gz,kit_14dpi_1_S1_L002_I1_001.fastq.gz kit_14dpi_1_S1_L002_R1_001.fastq.gz kit_14dpi_1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,7583332548.0,57449489.0,GSM4340649 r2,0:8 1:98 2:26,A:2187389217;C:1729495436;G:1735033918;T:1930459126;N:954851,8,98,26,,2187389217,1729495436,1735033918,1930459126,954851,SRX7806774,SRS6219809,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94677,0.00382,0.05499,0.00073,0.8799,0.99476,0.65903,0.57968,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56911,SRR11186478,SRX7806774,SRS6219809,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 1,GSM4340649,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340649,GSM4340649: kit 14dpi 1; Danio rerio; RNA Seq,GSM4340649,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340649,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 1 S1 L003 I1 001.fastq.gz   read2PairFiles=kit 14dpi 1 S1 L003 R2 001.fastq.gz   read3PairFiles=kit 14dpi 1 S1 L003 R1 001.fastq.gz,kit_14dpi_1_S1_L003_I1_001.fastq.gz kit_14dpi_1_S1_L003_R1_001.fastq.gz kit_14dpi_1_S1_L003_R2_001.fastq.gz,fastq fastq fastq,7743681660.0,58664255.0,GSM4340649 r3,0:8 1:98 2:26,A:2232465771;C:1767280975;G:1771189590;T:1972425675;N:319649,8,98,26,,2232465771,1767280975,1771189590,1972425675,319649,SRX7806774,SRS6219809,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94667,0.00396,0.05446,0.00069,0.87898,0.99435,0.67449,0.58166,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56912,SRR11186479,SRX7806774,SRS6219809,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 14dpi 1,GSM4340649,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 14dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340649,GSM4340649: kit 14dpi 1; Danio rerio; RNA Seq,GSM4340649,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340649,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 14dpi 1 S1 L004 I1 001.fastq.gz   read2PairFiles=kit 14dpi 1 S1 L004 R2 001.fastq.gz   read3PairFiles=kit 14dpi 1 S1 L004 R1 001.fastq.gz,kit_14dpi_1_S1_L004_I1_001.fastq.gz kit_14dpi_1_S1_L004_R1_001.fastq.gz kit_14dpi_1_S1_L004_R2_001.fastq.gz,fastq fastq fastq,7578751620.0,57414785.0,GSM4340649 r4,0:8 1:98 2:26,A:2186149125;C:1727568946;G:1736320769;T:1928275304;N:437476,8,98,26,,2186149125,1727568946,1736320769,1928275304,437476,SRX7806774,SRS6219809,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94703,0.00424,0.05495,0.00079,0.87998,0.99427,0.66208,0.59062,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56913,SRR11186472,SRX7806773,SRS6219808,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 2,GSM4340648,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340648,GSM4340648: kit 7dpi 2; Danio rerio; RNA Seq,GSM4340648,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340648,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 2 S2 L001 I1 001.fastq.gz   read2PairFiles=kit 7dpi 2 S2 L001 R2 001.fastq.gz   read3PairFiles=kit 7dpi 2 S2 L001 R1 001.fastq.gz,kit_7dpi_2_S2_L001_R2_001.fastq.gz kit_7dpi_2_S2_L001_R1_001.fastq.gz kit_7dpi_2_S2_L001_I1_001.fastq.gz,fastq fastq fastq,8209617240.0,62194070.0,GSM4340648 r1,0:8 1:98 2:26,A:2312735476;C:1884262957;G:1771663010;T:2240168892;N:786905,8,98,26,,2312735476,1884262957,1771663010,2240168892,786905,SRX7806773,SRS6219808,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.9403,0.0039,0.08407,0.00107,0.87513,0.99444,0.70468,0.49015,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56914,SRR11186473,SRX7806773,SRS6219808,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 2,GSM4340648,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340648,GSM4340648: kit 7dpi 2; Danio rerio; RNA Seq,GSM4340648,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340648,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 2 S2 L002 I1 001.fastq.gz   read2PairFiles=kit 7dpi 2 S2 L002 R2 001.fastq.gz   read3PairFiles=kit 7dpi 2 S2 L002 R1 001.fastq.gz,kit_7dpi_2_S2_L002_R2_001.fastq.gz kit_7dpi_2_S2_L002_R1_001.fastq.gz kit_7dpi_2_S2_L002_I1_001.fastq.gz,fastq fastq fastq,8149773456.0,61740708.0,GSM4340648 r2,0:8 1:98 2:26,A:2297785088;C:1868951676;G:1761075739;T:2221123916;N:837037,8,98,26,,2297785088,1868951676,1761075739,2221123916,837037,SRX7806773,SRS6219808,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94004,0.00406,0.08442,0.00106,0.87566,0.99393,0.78111,0.5533,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56915,SRR11186474,SRX7806773,SRS6219808,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 2,GSM4340648,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340648,GSM4340648: kit 7dpi 2; Danio rerio; RNA Seq,GSM4340648,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340648,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 2 S2 L003 I1 001.fastq.gz   read2PairFiles=kit 7dpi 2 S2 L003 R2 001.fastq.gz   read3PairFiles=kit 7dpi 2 S2 L003 R1 001.fastq.gz,kit_7dpi_2_S2_L003_R2_001.fastq.gz kit_7dpi_2_S2_L003_R1_001.fastq.gz kit_7dpi_2_S2_L003_I1_001.fastq.gz,fastq fastq fastq,8243556948.0,62451189.0,GSM4340648 r3,0:8 1:98 2:26,A:2326108259;C:1894650954;G:1773613791;T:2248841792;N:342152,8,98,26,,2326108259,1894650954,1773613791,2248841792,342152,SRX7806773,SRS6219808,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94077,0.00362,0.0843,0.00087,0.87519,0.99427,0.78241,0.49397,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56916,SRR11186475,SRX7806773,SRS6219808,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 2,GSM4340648,,source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 7dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340648,GSM4340648: kit 7dpi 2; Danio rerio; RNA Seq,GSM4340648,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340648,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 2 S2 L004 I1 001.fastq.gz   read2PairFiles=kit 7dpi 2 S2 L004 R2 001.fastq.gz   read3PairFiles=kit 7dpi 2 S2 L004 R1 001.fastq.gz,kit_7dpi_2_S2_L004_R2_001.fastq.gz kit_7dpi_2_S2_L004_R1_001.fastq.gz kit_7dpi_2_S2_L004_I1_001.fastq.gz,fastq fastq fastq,8122026396.0,61530503.0,GSM4340648 r4,0:8 1:98 2:26,A:2292564058;C:1865394324;G:1748553623;T:2215055354;N:459037,8,98,26,,2292564058,1865394324,1748553623,2215055354,459037,SRX7806773,SRS6219808,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.94042,0.00377,0.0841,0.00088,0.87592,0.99421,0.78064,0.50766,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56917,SRR11186468,SRX7806772,SRS6219807,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 1,GSM4340647,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340647,GSM4340647: kit 7dpi 1; Danio rerio; RNA Seq,GSM4340647,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340647,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 1 S1 L001 I1 001.fastq.gz   read2PairFiles=kit 7dpi 1 S1 L001 R2 001.fastq.gz   read3PairFiles=kit 7dpi 1 S1 L001 R1 001.fastq.gz,kit_7dpi_1_S1_L001_R2_001.fastq.gz kit_7dpi_1_S1_L001_R1_001.fastq.gz kit_7dpi_1_S1_L001_I1_001.fastq.gz,fastq fastq fastq,14539671564.0,110149027.0,GSM4340647 r1,0:8 1:98 2:26,A:4303751392;C:3293380661;G:3090073419;T:3847299815;N:5166277,8,98,26,,4303751392,3293380661,3090073419,3847299815,5166277,SRX7806772,SRS6219807,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.91778,0.00412,0.10274,0.00125,0.91516,0.99563,0.7683,0.69215,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56918,SRR11186469,SRX7806772,SRS6219807,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 1,GSM4340647,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340647,GSM4340647: kit 7dpi 1; Danio rerio; RNA Seq,GSM4340647,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340647,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 1 S1 L002 I1 001.fastq.gz   read2PairFiles=kit 7dpi 1 S1 L002 R2 001.fastq.gz   read3PairFiles=kit 7dpi 1 S1 L002 R1 001.fastq.gz,kit_7dpi_1_S1_L002_R2_001.fastq.gz kit_7dpi_1_S1_L002_R1_001.fastq.gz kit_7dpi_1_S1_L002_I1_001.fastq.gz,fastq fastq fastq,14381477484.0,108950587.0,GSM4340647 r2,0:8 1:98 2:26,A:4252877586;C:3257974495;G:3066131341;T:3798332536;N:6161526,8,98,26,,4252877586,3257974495,3066131341,3798332536,6161526,SRX7806772,SRS6219807,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.93766,0.00405,0.10586,0.00112,0.91685,0.99594,0.75009,0.72137,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56919,SRR11186470,SRX7806772,SRS6219807,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 1,GSM4340647,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340647,GSM4340647: kit 7dpi 1; Danio rerio; RNA Seq,GSM4340647,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340647,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 1 S1 L003 I1 001.fastq.gz   read2PairFiles=kit 7dpi 1 S1 L003 R2 001.fastq.gz   read3PairFiles=kit 7dpi 1 S1 L003 R1 001.fastq.gz,kit_7dpi_1_S1_L003_R2_001.fastq.gz kit_7dpi_1_S1_L003_R1_001.fastq.gz kit_7dpi_1_S1_L003_I1_001.fastq.gz,fastq fastq fastq,14591543736.0,110541998.0,GSM4340647 r3,0:8 1:98 2:26,A:4299018223;C:3311116432;G:3122793782;T:3856414404;N:2200895,8,98,26,,4299018223,3311116432,3122793782,3856414404,2200895,SRX7806772,SRS6219807,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.92239,0.00378,0.10228,0.00109,0.91437,0.99588,0.80184,0.70502,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56920,SRR11186471,SRX7806772,SRS6219807,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 7dpi 1,GSM4340647,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 7dpi 1,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340647,GSM4340647: kit 7dpi 1; Danio rerio; RNA Seq,GSM4340647,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340647,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 7dpi 1 S1 L004 I1 001.fastq.gz   read2PairFiles=kit 7dpi 1 S1 L004 R2 001.fastq.gz   read3PairFiles=kit 7dpi 1 S1 L004 R1 001.fastq.gz,kit_7dpi_1_S1_L004_R2_001.fastq.gz kit_7dpi_1_S1_L004_R1_001.fastq.gz kit_7dpi_1_S1_L004_I1_001.fastq.gz,fastq fastq fastq,14355509652.0,108753861.0,GSM4340647 r4,0:8 1:98 2:26,A:4247884521;C:3258701239;G:3054676665;T:3791553561;N:2693666,8,98,26,,4247884521,3258701239,3054676665,3791553561,2693666,SRX7806772,SRS6219807,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.93467,0.00399,0.1104,0.00109,0.92389,0.99569,0.77957,0.71011,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56921,SRR11186464,SRX7806771,SRS6219806,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 2dpi 2,GSM4340646,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 2dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340646,GSM4340646: kit 2dpi 2; Danio rerio; RNA Seq,GSM4340646,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340646,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 2dpi 2 S2 L001 I1 001.fastq.gz   read2PairFiles=kit 2dpi 2 S2 L001 R2 001.fastq.gz   read3PairFiles=kit 2dpi 2 S2 L001 R1 001.fastq.gz,kit_2dpi_2_S2_L001_R2_001.fastq.gz kit_2dpi_2_S2_L001_R1_001.fastq.gz kit_2dpi_2_S2_L001_I1_001.fastq.gz,fastq fastq fastq,7945001988.0,60189409.0,GSM4340646 r1,0:8 1:98 2:26,A:2265931188;C:1792882917;G:1722295921;T:2158777897;N:5114065,8,98,26,,2265931188,1792882917,1722295921,2158777897,5114065,SRX7806771,SRS6219806,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.9338,0.00372,0.10853,0.0011,0.86369,0.99397,0.70558,0.48333,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System
56922,SRR11186465,SRX7806771,SRS6219806,SRP250827,PRJNA608912,Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq],GSE145980,Transcriptome Analysis,Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System.,parent bioproject:PRJNA608906,pubmed:34523214,,kit 2dpi 2,GSM4340646,,source name:kit 2dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,kit 2dpi 2,I1 8 bp sample barcode  R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed  debarcoded  mapped to UCSC DanRer10 genome  and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant  respectively,kit 2dpi nonCMs,Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,Zebrafish were raised and maintained under standard laboratory conditions.,genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs,GSM4340646,GSM4340646: kit 2dpi 2; Danio rerio; RNA Seq,GSM4340646,,1,Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5.,GEO Accession:GSM4340646,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP250827,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=kit 2dpi 2 S2 L002 I1 001.fastq.gz   read2PairFiles=kit 2dpi 2 S2 L002 R2 001.fastq.gz   read3PairFiles=kit 2dpi 2 S2 L002 R1 001.fastq.gz,kit_2dpi_2_S2_L002_R2_001.fastq.gz kit_2dpi_2_S2_L002_R1_001.fastq.gz kit_2dpi_2_S2_L002_I1_001.fastq.gz,fastq fastq fastq,7653461772.0,57980771.0,GSM4340646 r2,0:8 1:98 2:26,A:2186861936;C:1727288709;G:1657411957;T:2077370359;N:4528811,8,98,26,,2186861936,1727288709,1657411957,2077370359,4528811,SRX7806771,SRS6219806,SRA1048427,GEO,University of North Carolina at Chapel Hill,2,0.93346,0.00364,0.1075,0.00107,0.8649,0.99444,0.75675,0.51172,98,26,B,T,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-02-26,Adult,Adult,Heart,Cardiovascular System