{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation_coarse = \"Cardiovascular System\"", "rows": [[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.", null, "pubmed:32094112", null, "Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq", "GSM3610371", null, "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", null, "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\u2019s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l 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\u00b0C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. 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\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m 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.\u00a0Using 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", null, "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", null, "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 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l 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\u00b0C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. 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\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m 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.\u00a0Using 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", null, "SRP186305", null, "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, null, 3868981340, 3004344480, 3173242889, 3705905113, 19257788, "SRX5392462", "SRS4380285", "SRA850447", "GEO", "Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital", 1, 0.91532, null, 0.07049, null, 0.82722, null, 0.50962, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:32094112", null, "Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq", "GSM3610371", null, "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", null, "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\u2019s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l 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\u00b0C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. 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\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m 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.\u00a0Using 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", null, "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", null, "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 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l 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\u00b0C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. 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\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m 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.\u00a0Using 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", null, "SRP186305", null, "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, null, 3921736827, 3045954411, 3216708567, 3758217760, 17487139, "SRX5392462", "SRS4380285", "SRA850447", "GEO", "Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital", 1, 0.91469, null, 0.06915, null, 0.82747, null, 0.49959, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-02-15", "Pharyngula", "Embryo", "Heart", "Cardiovascular System"], [55246, "SRR10203908", "SRX6923953", "SRS5454835", "SRP223736", "PRJNA575000", "\u00adrunx1 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", null, "pubmed:32341028", null, "587680 47", "GSM4101382", null, "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\u00b0C. 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 3\u02b9 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\u2009\u00b0C 14/10\u2009hours 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", null, "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\u00b0C. 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 3\u02b9 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", null, "SRP223736", null, "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, null, 2859438039, 2396178995, 2404795699, 2802486902, 4809925, "SRX6923953", "SRS5454835", "SRA969982", "GEO", "Haematology, University of Cambridge", 1, 0.89929, null, 0.09034, null, 0.8505, null, 0.53912, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2019-09-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [55247, "SRR10203907", "SRX6923952", "SRS5454834", "SRP223736", "PRJNA575000", "\u00adrunx1 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", null, "pubmed:32341028", null, "587680 46", "GSM4101381", null, "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\u00b0C. 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 3\u02b9 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\u2009\u00b0C 14/10\u2009hours 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", null, "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\u00b0C. 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 3\u02b9 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", null, "SRP223736", null, "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, null, 3276822567, 2531188698, 2569553917, 3166325098, 5316400, "SRX6923952", "SRS5454834", "SRA969982", "GEO", "Haematology, University of Cambridge", 1, 0.91155, null, 0.11038, null, 0.84143, null, 0.5481, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2019-09-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [55248, "SRR10203906", "SRX6923951", "SRS5454833", "SRP223736", "PRJNA575000", "\u00adrunx1 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", null, "pubmed:32341028", null, "587680 45", "GSM4101380", null, "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\u00b0C. 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 3\u02b9 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\u2009\u00b0C 14/10\u2009hours 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", null, "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\u00b0C. 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 3\u02b9 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", null, "SRP223736", null, "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, null, 3152110963, 2379819000, 2458427917, 3139288192, 5128920, "SRX6923951", "SRS5454833", "SRA969982", "GEO", "Haematology, University of Cambridge", 1, 0.90136, null, 0.13254, null, 0.84593, null, 0.51719, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, null, null, "10X Etv2 homozygous 20ss", "GSM4273675", null, "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", null, "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", null, "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", null, "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", null, "SRP242096", null, "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, null, 4380181360, 2963120216, 3162327779, 3757758592, 2052333, "SRX7568764", "SRS6004889", "SRA1026915", "GEO", "Cincinnati Children's Hospital", 1, 0.85534, null, 0.08164, null, 0.8504, null, 0.47433, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "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", null, null, null, "10X Etv2 homozygous 20ss", "GSM4273675", null, "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", null, "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", null, "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", null, "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", null, "SRP242096", null, "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, null, 4504330378, 3047430997, 3252225360, 3865730356, 2484999, "SRX7568764", "SRS6004889", "SRA1026915", "GEO", "Cincinnati Children's Hospital", 1, 0.85397, null, 0.08065, null, 0.85362, null, 0.47925, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "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", null, null, null, "10X Etv2 heterozygous 20ss", "GSM4273674", null, "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", null, "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", null, "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", null, "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", null, "SRP242096", null, "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, null, 4841927214, 3312520117, 3546106776, 4325878552, 2343195, "SRX7568763", "SRS6004888", "SRA1026915", "GEO", "Cincinnati Children's Hospital", 1, 0.85679, null, 0.0914, null, 0.84423, null, 0.50119, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "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", null, null, null, "10X Etv2 heterozygous 20ss", "GSM4273674", null, "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", null, "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", null, "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", null, "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", null, "SRP242096", null, "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, null, 4982587485, 3409998223, 3650593667, 4454135325, 2803662, "SRX7568763", "SRS6004888", "SRA1026915", "GEO", "Cincinnati Children's Hospital", 1, 0.85659, null, 0.09023, null, 0.84567, null, 0.51573, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "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", null, "kit 14dpi 2", "GSM4340650", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 2", "GSM4340650", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 2", "GSM4340650", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 2", "GSM4340650", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 1", "GSM4340649", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 1", "GSM4340649", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 1", "GSM4340649", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 14dpi 1", "GSM4340649", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 2", "GSM4340648", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 2", "GSM4340648", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 2", "GSM4340648", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 2", "GSM4340648", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 1", "GSM4340647", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 1", "GSM4340647", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 1", "GSM4340647", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 7dpi 1", "GSM4340647", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 2dpi 2", "GSM4340646", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "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", null, "kit 2dpi 2", "GSM4340646", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "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, null, 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", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56923, "SRR11186466", "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", null, "kit 2dpi 2", "GSM4340646", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 2 S2 L003 I1 001.fastq.gz read2PairFiles=kit 2dpi 2 S2 L003 R2 001.fastq.gz read3PairFiles=kit 2dpi 2 S2 L003 R1 001.fastq.gz", "kit_2dpi_2_S2_L003_R2_001.fastq.gz kit_2dpi_2_S2_L003_R1_001.fastq.gz kit_2dpi_2_S2_L003_I1_001.fastq.gz", "fastq fastq fastq", 7878896652.0, 59688611.0, "GSM4340646 r3", "0:8 1:98 2:26", "A:2252663509;C:1780602624;G:1704044502;T:2140942227;N:643790", 8, 98, 26, null, 2252663509, 1780602624, 1704044502, 2140942227, 643790, "SRX7806771", "SRS6219806", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93493, 0.00397, 0.10841, 0.00112, 0.86484, 0.99379, 0.71419, 0.51837, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56924, "SRR11186467", "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", null, "kit 2dpi 2", "GSM4340646", null, "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\u00b0C. 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", null, "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\u00b0C. 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", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 2 S2 L004 I1 001.fastq.gz read2PairFiles=kit 2dpi 2 S2 L004 R2 001.fastq.gz read3PairFiles=kit 2dpi 2 S2 L004 R1 001.fastq.gz", "kit_2dpi_2_S2_L004_R2_001.fastq.gz kit_2dpi_2_S2_L004_R1_001.fastq.gz kit_2dpi_2_S2_L004_I1_001.fastq.gz", "fastq fastq fastq", 7627841100.0, 57786675.0, "GSM4340646 r4", "0:8 1:98 2:26", "A:2180873889;C:1722667268;G:1651960229;T:2071564897;N:774817", 8, 98, 26, null, 2180873889, 1722667268, 1651960229, 2071564897, 774817, "SRX7806771", "SRS6219806", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93427, 0.00335, 0.10564, 0.00095, 0.8663, 0.99466, 0.80194, 0.52154, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56925, "SRR11186460", "SRX7806770", "SRS6219805", "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", null, "kit 2dpi 1", "GSM4340645", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit 2dpi 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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340645", "GSM4340645: kit 2dpi 1; Danio rerio; RNA Seq", "GSM4340645", null, "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\u00b0C. 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:GSM4340645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 1 S2 L001 I1 001.fastq.gz read2PairFiles=kit 2dpi 1 S2 L001 R2 001.fastq.gz read3PairFiles=kit 2dpi 1 S2 L001 R1 001.fastq.gz", "kit_2dpi_1_S2_L001_I1_001.fastq.gz kit_2dpi_1_S2_L001_R1_001.fastq.gz kit_2dpi_1_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 4505593224.0, 34133282.0, "GSM4340645 r1", "0:8 1:98 2:26", "A:1340016196;C:1006853278;G:902481177;T:1254220789;N:2021784", 8, 98, 26, null, 1340016196, 1006853278, 902481177, 1254220789, 2021784, "SRX7806770", "SRS6219805", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.937, 0.00304, 0.0888, 0.00115, 0.9572, 0.99553, 0.62068, 0.55786, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56926, "SRR11186461", "SRX7806770", "SRS6219805", "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", null, "kit 2dpi 1", "GSM4340645", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit 2dpi 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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340645", "GSM4340645: kit 2dpi 1; Danio rerio; RNA Seq", "GSM4340645", null, "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\u00b0C. 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:GSM4340645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 1 S2 L002 I1 001.fastq.gz read2PairFiles=kit 2dpi 1 S2 L002 R2 001.fastq.gz read3PairFiles=kit 2dpi 1 S2 L002 R1 001.fastq.gz", "kit_2dpi_1_S2_L002_R2_001.fastq.gz kit_2dpi_1_S2_L002_R1_001.fastq.gz kit_2dpi_1_S2_L002_I1_001.fastq.gz", "fastq fastq fastq", 6680806836.0, 50612173.0, "GSM4340645 r2", "0:8 1:98 2:26", "A:1913075284;C:1504704658;G:1453055624;T:1806419452;N:3551818", 8, 98, 26, null, 1913075284, 1504704658, 1453055624, 1806419452, 3551818, "SRX7806770", "SRS6219805", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.94722, 0.00434, 0.06874, 0.00096, 0.88288, 0.99241, 0.7245, 0.49032, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56927, "SRR11186462", "SRX7806770", "SRS6219805", "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", null, "kit 2dpi 1", "GSM4340645", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit 2dpi 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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340645", "GSM4340645: kit 2dpi 1; Danio rerio; RNA Seq", "GSM4340645", null, "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\u00b0C. 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:GSM4340645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 1 S2 L003 I1 001.fastq.gz read2PairFiles=kit 2dpi 1 S2 L003 R2 001.fastq.gz read3PairFiles=kit 2dpi 1 S2 L003 R1 001.fastq.gz", "kit_2dpi_1_S2_L003_R2_001.fastq.gz kit_2dpi_1_S2_L003_R1_001.fastq.gz kit_2dpi_1_S2_L003_I1_001.fastq.gz", "fastq fastq fastq", 4938718488.0, 37414534.0, "GSM4340645 r3", "0:8 1:98 2:26", "A:1454241893;C:1115338465;G:996018250;T:1370335155;N:2784725", 8, 98, 26, null, 1454241893, 1115338465, 996018250, 1370335155, 2784725, "SRX7806770", "SRS6219805", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.9206, 0.00345, 0.09726, 0.00095, 0.97467, 0.99492, 0.71526, 0.50577, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56928, "SRR11186463", "SRX7806770", "SRS6219805", "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", null, "kit 2dpi 1", "GSM4340645", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit 2dpi 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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340645", "GSM4340645: kit 2dpi 1; Danio rerio; RNA Seq", "GSM4340645", null, "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\u00b0C. 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:GSM4340645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 2dpi 1 S2 L004 I1 001.fastq.gz read2PairFiles=kit 2dpi 1 S2 L004 R2 001.fastq.gz read3PairFiles=kit 2dpi 1 S2 L004 R1 001.fastq.gz", "kit_2dpi_1_S2_L004_R2_001.fastq.gz kit_2dpi_1_S2_L004_R1_001.fastq.gz kit_2dpi_1_S2_L004_I1_001.fastq.gz", "fastq fastq fastq", 4606504716.0, 34897763.0, "GSM4340645 r4", "0:8 1:98 2:26", "A:1362535490;C:1033761123;G:926856517;T:1280842147;N:2509439", 8, 98, 26, null, 1362535490, 1033761123, 926856517, 1280842147, 2509439, "SRX7806770", "SRS6219805", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.9303, 0.00401, 0.09271, 0.00165, 0.97275, 0.99464, 0.72454, 0.50122, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56929, "SRR11186456", "SRX7806769", "SRS6219804", "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", null, "kit uninjuried", "GSM4340644", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit uninjuried", "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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340644", "GSM4340644: kit uninjuried; Danio rerio; RNA Seq", "GSM4340644", null, "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\u00b0C. 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:GSM4340644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit uninjuried S2 L001 I1 001.fastq.gz read2PairFiles=kit uninjuried S2 L001 R2 001.fastq.gz read3PairFiles=kit uninjuried S2 L001 R1 001.fastq.gz", "kit_uninjuried_S2_L001_I1_001.fastq.gz kit_uninjuried_S2_L001_R1_001.fastq.gz kit_uninjuried_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 6216946428.0, 47098079.0, "GSM4340644 r1", "0:8 1:98 2:26", "A:1863028152;C:1374649093;G:1346758691;T:1620114636;N:12395856", 8, 98, 26, null, 1863028152, 1374649093, 1346758691, 1620114636, 12395856, "SRX7806769", "SRS6219804", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93361, 0.00419, 0.12367, 0.00119, 0.92581, 0.99452, 0.74507, 0.6528, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56930, "SRR11186457", "SRX7806769", "SRS6219804", "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", null, "kit uninjuried", "GSM4340644", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit uninjuried", "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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340644", "GSM4340644: kit uninjuried; Danio rerio; RNA Seq", "GSM4340644", null, "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\u00b0C. 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:GSM4340644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit uninjuried S2 L002 I1 001.fastq.gz read2PairFiles=kit uninjuried S2 L002 R2 001.fastq.gz read3PairFiles=kit uninjuried S2 L002 R1 001.fastq.gz", "kit_uninjuried_S2_L002_I1_001.fastq.gz kit_uninjuried_S2_L002_R1_001.fastq.gz kit_uninjuried_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 7418805504.0, 56203072.0, "GSM4340644 r2", "0:8 1:98 2:26", "A:2186428627;C:1644582275;G:1648919475;T:1923697162;N:15177965", 8, 98, 26, null, 2186428627, 1644582275, 1648919475, 1923697162, 15177965, "SRX7806769", "SRS6219804", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93011, 0.00444, 0.10994, 0.00127, 0.88424, 0.99464, 0.7532, 0.63435, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56931, "SRR11186458", "SRX7806769", "SRS6219804", "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", null, "kit uninjuried", "GSM4340644", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit uninjuried", "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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340644", "GSM4340644: kit uninjuried; Danio rerio; RNA Seq", "GSM4340644", null, "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\u00b0C. 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:GSM4340644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit uninjuried S2 L003 I1 001.fastq.gz read2PairFiles=kit uninjuried S2 L003 R2 001.fastq.gz read3PairFiles=kit uninjuried S2 L003 R1 001.fastq.gz", "kit_uninjuried_S2_L003_I1_001.fastq.gz kit_uninjuried_S2_L003_R1_001.fastq.gz kit_uninjuried_S2_L003_R2_001.fastq.gz", "fastq fastq fastq", 5876457840.0, 44518620.0, "GSM4340644 r3", "0:8 1:98 2:26", "A:1773407621;C:1297485163;G:1268443329;T:1532556477;N:4565250", 8, 98, 26, null, 1773407621, 1297485163, 1268443329, 1532556477, 4565250, "SRX7806769", "SRS6219804", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93506, 0.00385, 0.1215, 0.00109, 0.92429, 0.99513, 0.74856, 0.65995, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56932, "SRR11186459", "SRX7806769", "SRS6219804", "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", null, "kit uninjuried", "GSM4340644", null, "source name:kit unjuried nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "kit uninjuried", "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 unjuried 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\u00b0C. 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:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340644", "GSM4340644: kit uninjuried; Danio rerio; RNA Seq", "GSM4340644", null, "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\u00b0C. 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:GSM4340644", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit uninjuried S2 L004 I1 001.fastq.gz read2PairFiles=kit uninjuried S2 L004 R2 001.fastq.gz read3PairFiles=kit uninjuried S2 L004 R1 001.fastq.gz", "kit_uninjuried_S2_L004_I1_001.fastq.gz kit_uninjuried_S2_L004_R1_001.fastq.gz kit_uninjuried_S2_L004_R2_001.fastq.gz", "fastq fastq fastq", 6506980392.0, 49295306.0, "GSM4340644 r4", "0:8 1:98 2:26", "A:1940034424;C:1438363337;G:1427723458;T:1695277029;N:5582144", 8, 98, 26, null, 1940034424, 1438363337, 1427723458, 1695277029, 5582144, "SRX7806769", "SRS6219804", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93606, 0.00427, 0.11306, 0.00131, 0.90321, 0.99519, 0.71779, 0.65103, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56933, "SRR11186452", "SRX7806768", "SRS6219803", "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", null, "wt 14dpi", "GSM4340643", null, "source name:wt 14dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 14dpi", "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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340643", "GSM4340643: wt 14dpi; Danio rerio; RNA Seq", "GSM4340643", null, "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\u00b0C. 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:GSM4340643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 14dpi S2 L001 I1 001.fastq.gz read2PairFiles=wt 14dpi S2 L001 R2 001.fastq.gz read3PairFiles=wt 14dpi S2 L001 R1 001.fastq.gz", "wt_14dpi_S2_L001_R2_001.fastq.gz wt_14dpi_S2_L001_R1_001.fastq.gz wt_14dpi_S2_L001_I1_001.fastq.gz", "fastq fastq fastq", 7075492512.0, 53602216.0, "GSM4340643 r1", "0:8 1:98 2:26", "A:2058555543;C:1617470815;G:1581334689;T:1817107068;N:1024397", 8, 98, 26, null, 2058555543, 1617470815, 1581334689, 1817107068, 1024397, "SRX7806768", "SRS6219803", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95408, 0.00374, 0.05347, 0.00084, 0.87931, 0.99486, 0.78771, 0.64097, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56934, "SRR11186453", "SRX7806768", "SRS6219803", "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", null, "wt 14dpi", "GSM4340643", null, "source name:wt 14dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 14dpi", "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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340643", "GSM4340643: wt 14dpi; Danio rerio; RNA Seq", "GSM4340643", null, "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\u00b0C. 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:GSM4340643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 14dpi S2 L002 I1 001.fastq.gz read2PairFiles=wt 14dpi S2 L002 R2 001.fastq.gz read3PairFiles=wt 14dpi S2 L002 R1 001.fastq.gz", "wt_14dpi_S2_L002_I1_001.fastq.gz wt_14dpi_S2_L002_R1_001.fastq.gz wt_14dpi_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 6962878428.0, 52749079.0, "GSM4340643 r2", "0:8 1:98 2:26", "A:2027066021;C:1591852290;G:1557637060;T:1785440563;N:882494", 8, 98, 26, null, 2027066021, 1591852290, 1557637060, 1785440563, 882494, "SRX7806768", "SRS6219803", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95448, 0.0036, 0.05219, 0.00076, 0.88312, 0.99553, 0.79306, 0.58015, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56935, "SRR11186454", "SRX7806768", "SRS6219803", "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", null, "wt 14dpi", "GSM4340643", null, "source name:wt 14dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 14dpi", "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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340643", "GSM4340643: wt 14dpi; Danio rerio; RNA Seq", "GSM4340643", null, "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\u00b0C. 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:GSM4340643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 14dpi S2 L003 I1 001.fastq.gz read2PairFiles=wt 14dpi S2 L003 R2 001.fastq.gz read3PairFiles=wt 14dpi S2 L003 R1 001.fastq.gz", "wt_14dpi_S2_L003_I1_001.fastq.gz wt_14dpi_S2_L003_R1_001.fastq.gz wt_14dpi_S2_L003_R2_001.fastq.gz", "fastq fastq fastq", 7105172316.0, 53827063.0, "GSM4340643 r3", "0:8 1:98 2:26", "A:2068203912;C:1625572023;G:1587751502;T:1823353695;N:291184", 8, 98, 26, null, 2068203912, 1625572023, 1587751502, 1823353695, 291184, "SRX7806768", "SRS6219803", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95384, 0.00354, 0.05316, 0.00082, 0.88252, 0.99537, 0.78317, 0.62874, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56936, "SRR11186455", "SRX7806768", "SRS6219803", "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", null, "wt 14dpi", "GSM4340643", null, "source name:wt 14dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 14dpi", "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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:14 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340643", "GSM4340643: wt 14dpi; Danio rerio; RNA Seq", "GSM4340643", null, "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\u00b0C. 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:GSM4340643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 14dpi S2 L004 I1 001.fastq.gz read2PairFiles=wt 14dpi S2 L004 R2 001.fastq.gz read3PairFiles=wt 14dpi S2 L004 R1 001.fastq.gz", "wt_14dpi_S2_L004_I1_001.fastq.gz wt_14dpi_S2_L004_R1_001.fastq.gz wt_14dpi_S2_L004_R2_001.fastq.gz", "fastq fastq fastq", 6956560512.0, 52701216.0, "GSM4340643 r4", "0:8 1:98 2:26", "A:2025894611;C:1589604937;G:1557595489;T:1783071464;N:394011", 8, 98, 26, null, 2025894611, 1589604937, 1557595489, 1783071464, 394011, "SRX7806768", "SRS6219803", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95318, 0.00361, 0.05119, 0.00082, 0.88189, 0.99535, 0.73231, 0.61598, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56937, "SRR11186448", "SRX7806767", "SRS6219802", "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", null, "wt 7dpi 2", "GSM4340642", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340642", "GSM4340642: wt 7dpi 2; Danio rerio; RNA Seq", "GSM4340642", null, "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\u00b0C. 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:GSM4340642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 2 S1 L001 I1 001.fastq.gz read2PairFiles=wt 7dpi 2 S1 L001 R2 001.fastq.gz read3PairFiles=wt 7dpi 2 S1 L001 R1 001.fastq.gz", "wt_7dpi_2_S1_L001_I1_001.fastq.gz wt_7dpi_2_S1_L001_R1_001.fastq.gz wt_7dpi_2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 8103978564.0, 61393777.0, "GSM4340642 r1", "0:8 1:98 2:26", "A:2293675513;C:1842636410;G:1736613655;T:2230280009;N:772977", 8, 98, 26, null, 2293675513, 1842636410, 1736613655, 2230280009, 772977, "SRX7806767", "SRS6219802", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.94143, 0.00401, 0.08071, 0.00104, 0.86833, 0.99352, 0.74136, 0.45, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56938, "SRR11186449", "SRX7806767", "SRS6219802", "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", null, "wt 7dpi 2", "GSM4340642", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340642", "GSM4340642: wt 7dpi 2; Danio rerio; RNA Seq", "GSM4340642", null, "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\u00b0C. 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:GSM4340642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 2 S1 L002 I1 001.fastq.gz read2PairFiles=wt 7dpi 2 S1 L002 R2 001.fastq.gz read3PairFiles=wt 7dpi 2 S1 L002 R1 001.fastq.gz", "wt_7dpi_2_S1_L002_I1_001.fastq.gz wt_7dpi_2_S1_L002_R1_001.fastq.gz wt_7dpi_2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 8045377560.0, 60949830.0, "GSM4340642 r2", "0:8 1:98 2:26", "A:2278993572;C:1827774377;G:1726530084;T:2211249594;N:829933", 8, 98, 26, null, 2278993572, 1827774377, 1726530084, 2211249594, 829933, "SRX7806767", "SRS6219802", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.9404, 0.00368, 0.08129, 0.00113, 0.87253, 0.99506, 0.74453, 0.47835, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56939, "SRR11186450", "SRX7806767", "SRS6219802", "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", null, "wt 7dpi 2", "GSM4340642", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340642", "GSM4340642: wt 7dpi 2; Danio rerio; RNA Seq", "GSM4340642", null, "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\u00b0C. 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:GSM4340642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 2 S1 L003 I1 001.fastq.gz read2PairFiles=wt 7dpi 2 S1 L003 R2 001.fastq.gz read3PairFiles=wt 7dpi 2 S1 L003 R1 001.fastq.gz", "wt_7dpi_2_S1_L003_I1_001.fastq.gz wt_7dpi_2_S1_L003_R1_001.fastq.gz wt_7dpi_2_S1_L003_R2_001.fastq.gz", "fastq fastq fastq", 8158671444.0, 61808117.0, "GSM4340642 r3", "0:8 1:98 2:26", "A:2313025782;C:1857940322;G:1743240566;T:2244120056;N:344718", 8, 98, 26, null, 2313025782, 1857940322, 1743240566, 2244120056, 344718, "SRX7806767", "SRS6219802", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.94124, 0.00383, 0.07996, 0.00101, 0.86963, 0.99411, 0.74608, 0.423, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56940, "SRR11186451", "SRX7806767", "SRS6219802", "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", null, "wt 7dpi 2", "GSM4340642", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340642", "GSM4340642: wt 7dpi 2; Danio rerio; RNA Seq", "GSM4340642", null, "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\u00b0C. 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:GSM4340642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 2 S1 L004 I1 001.fastq.gz read2PairFiles=wt 7dpi 2 S1 L004 R2 001.fastq.gz read3PairFiles=wt 7dpi 2 S1 L004 R1 001.fastq.gz", "wt_7dpi_2_S1_L004_I1_001.fastq.gz wt_7dpi_2_S1_L004_R1_001.fastq.gz wt_7dpi_2_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 8030545776.0, 60837468.0, "GSM4340642 r4", "0:8 1:98 2:26", "A:2277649826;C:1827073179;G:1716738749;T:2208632369;N:451653", 8, 98, 26, null, 2277649826, 1827073179, 1716738749, 2208632369, 451653, "SRX7806767", "SRS6219802", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.9412, 0.00373, 0.08165, 0.00106, 0.87089, 0.99446, 0.74754, 0.45962, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56941, "SRR11186444", "SRX7806766", "SRS6219801", "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", null, "wt 7dpi 1", "GSM4340641", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340641", "GSM4340641: wt 7dpi 1; Danio rerio; RNA Seq", "GSM4340641", null, "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\u00b0C. 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:GSM4340641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 1 S1 L001 I1 001.fastq.gz read2PairFiles=wt 7dpi 1 S1 L001 R2 001.fastq.gz read3PairFiles=wt 7dpi 1 S1 L001 R1 001.fastq.gz", "wt_7dpi_1_S1_L001_I1_001.fastq.gz wt_7dpi_1_S1_L001_R1_001.fastq.gz wt_7dpi_1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 15523767864.0, 117604302.0, "GSM4340641 r1", "0:8 1:98 2:26", "A:4562340103;C:3371610769;G:3580095025;T:3984508861;N:25213106", 8, 98, 26, null, 4562340103, 3371610769, 3580095025, 3984508861, 25213106, "SRX7806766", "SRS6219801", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.91762, 0.00191, 0.14433, 0.00078, 0.85368, 0.99683, 0.62416, 0.43062, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56942, "SRR11186445", "SRX7806766", "SRS6219801", "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", null, "wt 7dpi 1", "GSM4340641", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340641", "GSM4340641: wt 7dpi 1; Danio rerio; RNA Seq", "GSM4340641", null, "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\u00b0C. 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:GSM4340641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 1 S1 L002 I1 001.fastq.gz read2PairFiles=wt 7dpi 1 S1 L002 R2 001.fastq.gz read3PairFiles=wt 7dpi 1 S1 L002 R1 001.fastq.gz", "wt_7dpi_1_S1_L002_I1_001.fastq.gz wt_7dpi_1_S1_L002_R1_001.fastq.gz wt_7dpi_1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 15169047960.0, 114917030.0, "GSM4340641 r2", "0:8 1:98 2:26", "A:4497460313;C:3290833294;G:3451861471;T:3904066251;N:24826631", 8, 98, 26, null, 4497460313, 3290833294, 3451861471, 3904066251, 24826631, "SRX7806766", "SRS6219801", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.91837, 0.00189, 0.15106, 0.00083, 0.85985, 0.99693, 0.61056, 0.38974, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56943, "SRR11186446", "SRX7806766", "SRS6219801", "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", null, "wt 7dpi 1", "GSM4340641", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340641", "GSM4340641: wt 7dpi 1; Danio rerio; RNA Seq", "GSM4340641", null, "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\u00b0C. 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:GSM4340641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 1 S1 L003 I1 001.fastq.gz read2PairFiles=wt 7dpi 1 S1 L003 R2 001.fastq.gz read3PairFiles=wt 7dpi 1 S1 L003 R1 001.fastq.gz", "wt_7dpi_1_S1_L003_I1_001.fastq.gz wt_7dpi_1_S1_L003_R1_001.fastq.gz wt_7dpi_1_S1_L003_R2_001.fastq.gz", "fastq fastq fastq", 14681255424.0, 111221632.0, "GSM4340641 r3", "0:8 1:98 2:26", "A:4339122253;C:3177987024;G:3373047617;T:3780886290;N:10212240", 8, 98, 26, null, 4339122253, 3177987024, 3373047617, 3780886290, 10212240, "SRX7806766", "SRS6219801", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.91755, 0.00184, 0.14457, 0.00073, 0.85782, 0.99679, 0.61577, 0.39603, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56944, "SRR11186447", "SRX7806766", "SRS6219801", "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", null, "wt 7dpi 1", "GSM4340641", null, "source name:wt 7dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340641", "GSM4340641: wt 7dpi 1; Danio rerio; RNA Seq", "GSM4340641", null, "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\u00b0C. 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:GSM4340641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 7dpi 1 S1 L004 I1 001.fastq.gz read2PairFiles=wt 7dpi 1 S1 L004 R2 001.fastq.gz read3PairFiles=wt 7dpi 1 S1 L004 R1 001.fastq.gz", "wt_7dpi_1_S1_L004_I1_001.fastq.gz wt_7dpi_1_S1_L004_R1_001.fastq.gz wt_7dpi_1_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 14853523476.0, 112526693.0, "GSM4340641 r4", "0:8 1:98 2:26", "A:4399028476;C:3217807905;G:3398336241;T:3827406331;N:10944523", 8, 98, 26, null, 4399028476, 3217807905, 3398336241, 3827406331, 10944523, "SRX7806766", "SRS6219801", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.91837, 0.00195, 0.15019, 0.00071, 0.86243, 0.99667, 0.59247, 0.42608, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56945, "SRR11186440", "SRX7806765", "SRS6219800", "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", null, "wt 2dpi 2", "GSM4340640", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340640", "GSM4340640: wt 2dpi 2; Danio rerio; RNA Seq", "GSM4340640", null, "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\u00b0C. 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:GSM4340640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 2 S1 L001 I1 001.fastq.gz read2PairFiles=wt 2dpi 2 S1 L001 R2 001.fastq.gz read3PairFiles=wt 2dpi 2 S1 L001 R1 001.fastq.gz", "wt_2dpi_2_S1_L001_I1_001.fastq.gz wt_2dpi_2_S1_L001_R1_001.fastq.gz wt_2dpi_2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 8015597964.0, 60724227.0, "GSM4340640 r1", "0:8 1:98 2:26", "A:2263773021;C:1769604386;G:1780400403;T:2196673714;N:5146440", 8, 98, 26, null, 2263773021, 1769604386, 1780400403, 2196673714, 5146440, "SRX7806765", "SRS6219800", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93831, 0.00411, 0.10094, 0.00108, 0.84145, 0.99299, 0.64629, 0.42314, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56946, "SRR11186441", "SRX7806765", "SRS6219800", "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", null, "wt 2dpi 2", "GSM4340640", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340640", "GSM4340640: wt 2dpi 2; Danio rerio; RNA Seq", "GSM4340640", null, "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\u00b0C. 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:GSM4340640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 2 S1 L002 I1 001.fastq.gz read2PairFiles=wt 2dpi 2 S1 L002 R2 001.fastq.gz read3PairFiles=wt 2dpi 2 S1 L002 R1 001.fastq.gz", "wt_2dpi_2_S1_L002_I1_001.fastq.gz wt_2dpi_2_S1_L002_R1_001.fastq.gz wt_2dpi_2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 7713765444.0, 58437617.0, "GSM4340640 r2", "0:8 1:98 2:26", "A:2182627174;C:1703455011;G:1711356046;T:2111750665;N:4576548", 8, 98, 26, null, 2182627174, 1703455011, 1711356046, 2111750665, 4576548, "SRX7806765", "SRS6219800", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93833, 0.00451, 0.10034, 0.00122, 0.84198, 0.99245, 0.64001, 0.40066, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56947, "SRR11186442", "SRX7806765", "SRS6219800", "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", null, "wt 2dpi 2", "GSM4340640", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340640", "GSM4340640: wt 2dpi 2; Danio rerio; RNA Seq", "GSM4340640", null, "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\u00b0C. 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:GSM4340640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 2 S1 L003 I1 001.fastq.gz read2PairFiles=wt 2dpi 2 S1 L003 R2 001.fastq.gz read3PairFiles=wt 2dpi 2 S1 L003 R1 001.fastq.gz", "wt_2dpi_2_S1_L003_I1_001.fastq.gz wt_2dpi_2_S1_L003_R1_001.fastq.gz wt_2dpi_2_S1_L003_R2_001.fastq.gz", "fastq fastq fastq", 7935555936.0, 60117848.0, "GSM4340640 r3", "0:8 1:98 2:26", "A:2246437263;C:1754586444;G:1758645099;T:2175240854;N:646276", 8, 98, 26, null, 2246437263, 1754586444, 1758645099, 2175240854, 646276, "SRX7806765", "SRS6219800", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93699, 0.00437, 0.09969, 0.00126, 0.84216, 0.99261, 0.63955, 0.41754, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56948, "SRR11186443", "SRX7806765", "SRS6219800", "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", null, "wt 2dpi 2", "GSM4340640", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340640", "GSM4340640: wt 2dpi 2; Danio rerio; RNA Seq", "GSM4340640", null, "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\u00b0C. 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:GSM4340640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 2 S1 L004 I1 001.fastq.gz read2PairFiles=wt 2dpi 2 S1 L004 R2 001.fastq.gz read3PairFiles=wt 2dpi 2 S1 L004 R1 001.fastq.gz", "wt_2dpi_2_S1_L004_I1_001.fastq.gz wt_2dpi_2_S1_L004_R1_001.fastq.gz wt_2dpi_2_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 7687329804.0, 58237347.0, "GSM4340640 r4", "0:8 1:98 2:26", "A:2176198194;C:1698636400;G:1705642371;T:2106056521;N:796318", 8, 98, 26, null, 2176198194, 1698636400, 1705642371, 2106056521, 796318, "SRX7806765", "SRS6219800", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93969, 0.00452, 0.10035, 0.00119, 0.84258, 0.99224, 0.639, 0.45634, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56949, "SRR11186436", "SRX7806764", "SRS6219799", "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", null, "wt 2dpi 1", "GSM4340639", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 2dpi 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340639", "GSM4340639: wt 2dpi 1; Danio rerio; RNA Seq", "GSM4340639", null, "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\u00b0C. 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:GSM4340639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 1 S1 L001 I1 001.fastq.gz read2PairFiles=wt 2dpi 1 S1 L001 R2 001.fastq.gz read3PairFiles=wt 2dpi 1 S1 L001 R1 001.fastq.gz", "wt_2dpi_1_S1_L001_I1_001.fastq.gz wt_2dpi_1_S1_L001_R1_001.fastq.gz wt_2dpi_1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 4579570380.0, 34693715.0, "GSM4340639 r1", "0:8 1:98 2:26", "A:1374094252;C:985250840;G:943550816;T:1274583546;N:2090926", 8, 98, 26, null, 1374094252, 985250840, 943550816, 1274583546, 2090926, "SRX7806764", "SRS6219799", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.9156, 0.00353, 0.11506, 0.00125, 0.94582, 0.99423, 0.56873, 0.45454, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56950, "SRR11186437", "SRX7806764", "SRS6219799", "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", null, "wt 2dpi 1", "GSM4340639", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 2dpi 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340639", "GSM4340639: wt 2dpi 1; Danio rerio; RNA Seq", "GSM4340639", null, "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\u00b0C. 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:GSM4340639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 1 S1 L002 I1 001.fastq.gz read2PairFiles=wt 2dpi 1 S1 L002 R2 001.fastq.gz read3PairFiles=wt 2dpi 1 S1 L002 R1 001.fastq.gz", "wt_2dpi_1_S1_L002_R2_001.fastq.gz wt_2dpi_1_S1_L002_R1_001.fastq.gz wt_2dpi_1_S1_L002_I1_001.fastq.gz", "fastq fastq fastq", 6672349596.0, 50548103.0, "GSM4340639 r2", "0:8 1:98 2:26", "A:1919337442;C:1448659432;G:1499219188;T:1801543592;N:3589942", 8, 98, 26, null, 1919337442, 1448659432, 1499219188, 1801543592, 3589942, "SRX7806764", "SRS6219799", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.93122, 0.00559, 0.09595, 0.00126, 0.85382, 0.99017, 0.59938, 0.47395, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56951, "SRR11186438", "SRX7806764", "SRS6219799", "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", null, "wt 2dpi 1", "GSM4340639", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 2dpi 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340639", "GSM4340639: wt 2dpi 1; Danio rerio; RNA Seq", "GSM4340639", null, "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\u00b0C. 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:GSM4340639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 1 S1 L003 I1 001.fastq.gz read2PairFiles=wt 2dpi 1 S1 L003 R2 001.fastq.gz read3PairFiles=wt 2dpi 1 S1 L003 R1 001.fastq.gz", "wt_2dpi_1_S1_L003_R2_001.fastq.gz wt_2dpi_1_S1_L003_R1_001.fastq.gz wt_2dpi_1_S1_L003_I1_001.fastq.gz", "fastq fastq fastq", 5010538368.0, 37958624.0, "GSM4340639 r3", "0:8 1:98 2:26", "A:1486516966;C:1090877090;G:1041015601;T:1389312272;N:2816439", 8, 98, 26, null, 1486516966, 1090877090, 1041015601, 1389312272, 2816439, "SRX7806764", "SRS6219799", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.90367, 0.00461, 0.12339, 0.00126, 0.96796, 0.99237, 0.58399, 0.43781, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56952, "SRR11186439", "SRX7806764", "SRS6219799", "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", null, "wt 2dpi 1", "GSM4340639", null, "source name:wt 2dpi nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt 2dpi 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", "wt 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:2 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340639", "GSM4340639: wt 2dpi 1; Danio rerio; RNA Seq", "GSM4340639", null, "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\u00b0C. 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:GSM4340639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt 2dpi 1 S1 L004 I1 001.fastq.gz read2PairFiles=wt 2dpi 1 S1 L004 R2 001.fastq.gz read3PairFiles=wt 2dpi 1 S1 L004 R1 001.fastq.gz", "wt_2dpi_1_S1_L004_I1_001.fastq.gz wt_2dpi_1_S1_L004_R1_001.fastq.gz wt_2dpi_1_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 4692662832.0, 35550476.0, "GSM4340639 r4", "0:8 1:98 2:26", "A:1399253467;C:1014623753;G:971809736;T:1304405490;N:2570386", 8, 98, 26, null, 1399253467, 1014623753, 971809736, 1304405490, 2570386, "SRX7806764", "SRS6219799", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.90864, 0.00473, 0.12293, 0.00183, 0.96613, 0.99352, 0.567, 0.48995, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56953, "SRR11186432", "SRX7806763", "SRS6219798", "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", null, "wt unjuried 2", "GSM4340638", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340638", "GSM4340638: wt unjuried 2; Danio rerio; RNA Seq", "GSM4340638", null, "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\u00b0C. 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:GSM4340638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 2 S2 L001 I1 001.fastq.gz read2PairFiles=wt unjuried 2 S2 L001 R2 001.fastq.gz read3PairFiles=wt unjuried 2 S2 L001 R1 001.fastq.gz", "wt_unjuried_2_S2_L001_I1_001.fastq.gz wt_unjuried_2_S2_L001_R1_001.fastq.gz wt_unjuried_2_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 8586109092.0, 65046281.0, "GSM4340638 r1", "0:8 1:98 2:26", "A:2462343397;C:1964292937;G:1771382845;T:2383806369;N:4283544", 8, 98, 26, null, 2462343397, 1964292937, 1771382845, 2383806369, 4283544, "SRX7806763", "SRS6219798", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95666, 0.00313, 0.06956, 0.00086, 0.87752, 0.995, 0.80919, 0.47215, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56954, "SRR11186433", "SRX7806763", "SRS6219798", "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", null, "wt unjuried 2", "GSM4340638", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340638", "GSM4340638: wt unjuried 2; Danio rerio; RNA Seq", "GSM4340638", null, "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\u00b0C. 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:GSM4340638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 2 S2 L002 I1 001.fastq.gz read2PairFiles=wt unjuried 2 S2 L002 R2 001.fastq.gz read3PairFiles=wt unjuried 2 S2 L002 R1 001.fastq.gz", "wt_unjuried_2_S2_L002_I1_001.fastq.gz wt_unjuried_2_S2_L002_R1_001.fastq.gz wt_unjuried_2_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 8477619480.0, 64224390.0, "GSM4340638 r2", "0:8 1:98 2:26", "A:2433661984;C:1938464695;G:1749176984;T:2352210072;N:4105745", 8, 98, 26, null, 2433661984, 1938464695, 1749176984, 2352210072, 4105745, "SRX7806763", "SRS6219798", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.958, 0.0029, 0.06975, 0.00077, 0.87965, 0.99537, 0.80495, 0.51025, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56955, "SRR11186434", "SRX7806763", "SRS6219798", "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", null, "wt unjuried 2", "GSM4340638", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340638", "GSM4340638: wt unjuried 2; Danio rerio; RNA Seq", "GSM4340638", null, "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\u00b0C. 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:GSM4340638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 2 S2 L003 I1 001.fastq.gz read2PairFiles=wt unjuried 2 S2 L003 R2 001.fastq.gz read3PairFiles=wt unjuried 2 S2 L003 R1 001.fastq.gz", "wt_unjuried_2_S2_L003_I1_001.fastq.gz wt_unjuried_2_S2_L003_R1_001.fastq.gz wt_unjuried_2_S2_L003_R2_001.fastq.gz", "fastq fastq fastq", 8512597236.0, 64489373.0, "GSM4340638 r3", "0:8 1:98 2:26", "A:2443805472;C:1949708780;G:1754940767;T:2363871657;N:270560", 8, 98, 26, null, 2443805472, 1949708780, 1754940767, 2363871657, 270560, "SRX7806763", "SRS6219798", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95815, 0.00313, 0.0698, 0.00081, 0.87838, 0.99547, 0.80886, 0.50352, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56956, "SRR11186435", "SRX7806763", "SRS6219798", "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", null, "wt unjuried 2", "GSM4340638", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340638", "GSM4340638: wt unjuried 2; Danio rerio; RNA Seq", "GSM4340638", null, "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\u00b0C. 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:GSM4340638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 2 S2 L004 I1 001.fastq.gz read2PairFiles=wt unjuried 2 S2 L004 R2 001.fastq.gz read3PairFiles=wt unjuried 2 S2 L004 R1 001.fastq.gz", "wt_unjuried_2_S2_L004_I1_001.fastq.gz wt_unjuried_2_S2_L004_R1_001.fastq.gz wt_unjuried_2_S2_L004_R2_001.fastq.gz", "fastq fastq fastq", 8397023184.0, 63613812.0, "GSM4340638 r4", "0:8 1:98 2:26", "A:2408856254;C:1922136831;G:1734698855;T:2330973430;N:357814", 8, 98, 26, null, 2408856254, 1922136831, 1734698855, 2330973430, 357814, "SRX7806763", "SRS6219798", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95649, 0.00294, 0.07029, 0.00072, 0.87862, 0.99533, 0.80906, 0.48, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56957, "SRR11186428", "SRX7806762", "SRS6219797", "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", null, "wt unjuried 1", "GSM4340637", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340637", "GSM4340637: wt unjuried 1; Danio rerio; RNA Seq", "GSM4340637", null, "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\u00b0C. 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:GSM4340637", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 1 S1 L001 I1 001.fastq.gz read2PairFiles=wt unjuried 1 S1 L001 R2 001.fastq.gz read3PairFiles=wt unjuried 1 S1 L001 R1 001.fastq.gz", "wt_unjuried_1_S1_L001_I1_001.fastq.gz wt_unjuried_1_S1_L001_R1_001.fastq.gz wt_unjuried_1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 6554495508.0, 49655269.0, "GSM4340637 r1", "0:8 1:98 2:26", "A:1973180068;C:1515087793;G:1298002699;T:1755267717;N:12957231", 8, 98, 26, null, 1973180068, 1515087793, 1298002699, 1755267717, 12957231, "SRX7806762", "SRS6219797", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.97143, 0.0018, 0.04752, 0.00054, 0.95434, 0.99827, 0.89456, 0.7533, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56958, "SRR11186429", "SRX7806762", "SRS6219797", "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", null, "wt unjuried 1", "GSM4340637", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340637", "GSM4340637: wt unjuried 1; Danio rerio; RNA Seq", "GSM4340637", null, "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\u00b0C. 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:GSM4340637", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 1 S1 L002 I1 001.fastq.gz read2PairFiles=wt unjuried 1 S1 L002 R2 001.fastq.gz read3PairFiles=wt unjuried 1 S1 L002 R1 001.fastq.gz", "wt_unjuried_1_S1_L002_I1_001.fastq.gz wt_unjuried_1_S1_L002_R1_001.fastq.gz wt_unjuried_1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 7845462240.0, 59435320.0, "GSM4340637 r2", "0:8 1:98 2:26", "A:2321206636;C:1820412580;G:1593996895;T:2093839947;N:16006182", 8, 98, 26, null, 2321206636, 1820412580, 1593996895, 2093839947, 16006182, "SRX7806762", "SRS6219797", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95413, 0.00181, 0.04197, 0.00049, 0.92456, 0.99803, 0.8915, 0.79338, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56959, "SRR11186430", "SRX7806762", "SRS6219797", "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", null, "wt unjuried 1", "GSM4340637", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340637", "GSM4340637: wt unjuried 1; Danio rerio; RNA Seq", "GSM4340637", null, "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\u00b0C. 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:GSM4340637", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 1 S1 L003 I1 001.fastq.gz read2PairFiles=wt unjuried 1 S1 L003 R2 001.fastq.gz read3PairFiles=wt unjuried 1 S1 L003 R1 001.fastq.gz", "wt_unjuried_1_S1_L003_I1_001.fastq.gz wt_unjuried_1_S1_L003_R1_001.fastq.gz wt_unjuried_1_S1_L003_R2_001.fastq.gz", "fastq fastq fastq", 6191326020.0, 46903985.0, "GSM4340637 r3", "0:8 1:98 2:26", "A:1874982861;C:1430628344;G:1222110054;T:1658820113;N:4784648", 8, 98, 26, null, 1874982861, 1430628344, 1222110054, 1658820113, 4784648, "SRX7806762", "SRS6219797", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.97103, 0.00176, 0.04475, 0.0005, 0.95357, 0.99835, 0.89335, 0.70535, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [56960, "SRR11186431", "SRX7806762", "SRS6219797", "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", null, "wt unjuried 1", "GSM4340637", null, "source name:wt unjuried nonCMs|genotype/variation:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "wt unjuried 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", "wt unjuried 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\u00b0C. 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:wild type|age:4 month 6 month|treatment/timepoint:uninjured|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs", "GSM4340637", "GSM4340637: wt unjuried 1; Danio rerio; RNA Seq", "GSM4340637", null, "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\u00b0C. 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:GSM4340637", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250827", null, "loader:fastq load.py|options: readTypes=TBB read1PairFiles=wt unjuried 1 S1 L004 I1 001.fastq.gz read2PairFiles=wt unjuried 1 S1 L004 R2 001.fastq.gz read3PairFiles=wt unjuried 1 S1 L004 R1 001.fastq.gz", "wt_unjuried_1_S1_L004_I1_001.fastq.gz wt_unjuried_1_S1_L004_R1_001.fastq.gz wt_unjuried_1_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 6869608944.0, 52042492.0, "GSM4340637 r4", "0:8 1:98 2:26", "A:2055206077;C:1590432501;G:1378505037;T:1839610949;N:5854380", 8, 98, 26, null, 2055206077, 1590432501, 1378505037, 1839610949, 5854380, "SRX7806762", "SRS6219797", "SRA1048427", "GEO", "University of North Carolina at Chapel Hill", 2, 0.95239, 0.00174, 0.04314, 0.00038, 0.93994, 0.99823, 0.88199, 0.82644, 98, 26, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [61433, "SRR12764354", "SRX9235087", "SRS7468488", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr23", "GSM4815760", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:yes", "Injured heart Hr23", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:3|morphine treatment:yes", "GSM4815760", "GSM4815760: Injured heart Hr23; Danio rerio; RNA Seq", "GSM4815760", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286165", null, null, "Hr23_3dpi_R1.fastq.gz Hr23_3dpi_R2.fastq.gz", "fastq fastq", 27063420810.0, 196111745.0, "GSM4815760 r1", "0:28 1:110", "A:7265122388;C:6550817533;G:6174386431;T:7047552819;N:25541639", 28, 110, null, null, 7265122388, 6550817533, 6174386431, 7047552819, 25541639, "SRX9235087", "SRS7468488", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00601, 0.9705, 0.00198, 0.05295, 0.99527, 0.88674, 0.34788, 0.64434, 28, 110, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61434, "SRR12764353", "SRX9235086", "SRS7468487", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr18", "GSM4815759", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:yes", "Injured heart Hr18", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:15|morphine treatment:yes", "GSM4815759", "GSM4815759: Injured heart Hr18; Danio rerio; RNA Seq", "GSM4815759", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815759", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286165", null, null, "Hr18_15dpi_R1.fastq.gz Hr18_15dpi_R2.fastq.gz", "fastq fastq", 14033587036.0, 113174089.0, "GSM4815759 r1", "0:26 1:98", "A:3926691474;C:3392465101;G:2893406518;T:3814340568;N:6683375", 26, 98, null, null, 3926691474, 3392465101, 2893406518, 3814340568, 6683375, "SRX9235086", "SRS7468487", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00117, 0.95531, 0.00035, 0.03554, 0.9987, 0.91711, 0.69677, 0.73938, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61435, "SRR12764352", "SRX9235085", "SRS7468486", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr16", "GSM4815758", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:no", "Injured heart Hr16", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:15|morphine treatment:no", "GSM4815758", "GSM4815758: Injured heart Hr16; Danio rerio; RNA Seq", "GSM4815758", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815758", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286165", null, null, "Hr16_15dpi_R1.fastq.gz Hr16_15dpi_R2.fastq.gz", "fastq fastq", 13775817944.0, 111095306.0, "GSM4815758 r1", "0:26 1:98", "A:3909482860;C:3332944413;G:2709871622;T:3816877067;N:6641982", 26, 98, null, null, 3909482860, 3332944413, 2709871622, 3816877067, 6641982, "SRX9235085", "SRS7468486", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00134, 0.95426, 0.00032, 0.03245, 0.99876, 0.91403, 0.74242, 0.81839, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61436, "SRR12764351", "SRX9235084", "SRS7468485", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr15", "GSM4815757", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:yes", "Injured heart Hr15", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:7|morphine treatment:yes", "GSM4815757", "GSM4815757: Injured heart Hr15; Danio rerio; RNA Seq", "GSM4815757", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815757", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286165", null, null, "Hr15_7dpi_R1.fastq.gz Hr15_7dpi_R2.fastq.gz", "fastq fastq", 23195422020.0, 187059855.0, "GSM4815757 r1", "0:26 1:98", "A:6444667358;C:5404326039;G:5039988304;T:6295302014;N:11138305", 26, 98, null, null, 6444667358, 5404326039, 5039988304, 6295302014, 11138305, "SRX9235084", "SRS7468485", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00189, 0.94386, 0.00063, 0.08495, 0.99705, 0.86468, 0.46558, 0.61998, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61437, "SRR12764350", "SRX9235083", "SRS7468484", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr11", "GSM4815756", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:no", "Injured heart Hr11", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:3|morphine treatment:no", "GSM4815756", "GSM4815756: Injured heart Hr11; Danio rerio; RNA Seq", "GSM4815756", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815756", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286165", null, null, "Hr11_3dpi_R1.fastq.gz Hr11_3dpi_R2.fastq.gz", "fastq fastq", 23738913524.0, 191442851.0, "GSM4815756 r1", "0:26 1:98", "A:6705929352;C:5419341649;G:5248659082;T:6353580575;N:11402866", 26, 98, null, null, 6705929352, 5419341649, 5248659082, 6353580575, 11402866, "SRX9235083", "SRS7468484", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00205, 0.92741, 0.00075, 0.09217, 0.99693, 0.85985, 0.46031, 0.65994, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61438, "SRR12764349", "SRX9235082", "SRS7468483", "SRP286165", "PRJNA667006", "Morphine alleviates pain post heart cryonjury in zebrafish without xxx regeneration", "GSE158919", "Transcriptome Analysis", "Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish similarly to higher vertebrates also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not however take into account the adverse effects including pain that may potentially arise from these methodologies. Here we assess the effect of two analgesics lidocaine and morphine followed post the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology we show morphine but not lidocaine significantly improves animal welfare 6 hours post cryoinjury without xxx heart regeneration process. Altogether morphine should be considered as the analgesic of choice to reduce post surgical pain in adult zebrafish. Overall design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3 7 and 15 xxx post injury", null, "pubmed:35864193", null, "Injured heart Hr8", "GSM4815755", null, "source name:Zebrafish heart|tissue:heart|strain:AB|morphine treatment:no", "Injured heart Hr8", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Genome build: GRCz11 Supplementary files format and content: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names", "Zebrafish heart", "Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|strain:AB|xxx post injury dpi:7|morphine treatment:no", "GSM4815755", "GSM4815755: Injured heart Hr8; Danio rerio; RNA Seq", "GSM4815755", null, "1", "Single cell suspension were made using LiberaseTM in HBSS buffer Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4815755", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286165", null, null, "Hr8_7dpi_R1.fastq.gz Hr8_7dpi_R2.fastq.gz", "fastq fastq", 21580959924.0, 147814794.0, "GSM4815755 r1", "0:26 1:120", "A:6357310342;C:4599579096;G:4645633832;T:5971522599;N:6914055", 26, 120, null, null, 6357310342, 4599579096, 4645633832, 5971522599, 6914055, "SRX9235082", "SRS7468483", "SRA1136952", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00512, 0.93898, 0.00124, 0.12722, 0.99233, 0.8968, 0.35897, 0.58267, 26, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-02", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [61439, "SRR12774417", "SRX9244928", "SRS7477621", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr24 scar", "GSM4817985", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr24 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817985", "GSM4817985: Injured heart Hr24 scar; Danio rerio; RNA Seq", "GSM4817985", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr24_3dpi_scar_R1.fastq.gz Hr24_3dpi_scar_R2.fastq.gz", "fastq fastq", 2828825824.0, 19113688.0, "GSM4817985 r1", "0:28 1:120", "A:790413558;C:884432980;G:659992564;T:493271365;N:715357", 28, 120, null, null, 790413558, 884432980, 659992564, 493271365, 715357, "SRX9244928", "SRS7477621", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00036, 0.00627, 0.00031, 0.00011, 0.99983, 0.99788, 0.625, 0.30048, 28, 120, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61440, "SRR12774416", "SRX9244927", "SRS7477620", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr23 scar", "GSM4817984", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr23 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817984", "GSM4817984: Injured heart Hr23 scar; Danio rerio; RNA Seq", "GSM4817984", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817984", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr23_3dpi_scar_R1.fastq.gz Hr23_3dpi_scar_R2.fastq.gz", "fastq fastq", 2902344378.0, 21031481.0, "GSM4817984 r1", "0:28 1:110", "A:843360748;C:898248946;G:647278023;T:510839763;N:2616898", 28, 110, null, null, 843360748, 898248946, 647278023, 510839763, 2616898, "SRX9244927", "SRS7477620", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00033, 0.00151, 0.00023, 2e-05, 0.99983, 0.9991, 0.70588, 0.21951, 28, 110, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61441, "SRR12774415", "SRX9244926", "SRS7477619", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr22 scar", "GSM4817983", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr22 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817983", "GSM4817983: Injured heart Hr22 scar; Danio rerio; RNA Seq", "GSM4817983", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817983", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr22_3dpi_scar_R1.fastq.gz Hr22_3dpi_scar_R2.fastq.gz", "fastq fastq", 2035031904.0, 14746608.0, "GSM4817983 r1", "0:28 1:110", "A:591404487;C:634590764;G:453474751;T:353722751;N:1839151", 28, 110, null, null, 591404487, 634590764, 453474751, 353722751, 1839151, "SRX9244926", "SRS7477619", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00044, 0.00208, 0.00019, 2e-05, 0.99961, 0.99898, 0.43478, 0.38157, 28, 110, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61442, "SRR12774414", "SRX9244925", "SRS7477618", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr21 scar", "GSM4817982", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr21 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817982", "GSM4817982: Injured heart Hr21 scar; Danio rerio; RNA Seq", "GSM4817982", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr21_30dpi_scar_R1.fastq.gz Hr21_30dpi_scar_R2.fastq.gz", "fastq fastq", 1667556960.0, 13448040.0, "GSM4817982 r1", "0:26 1:98", "A:483368482;C:520890813;G:365891957;T:296624399;N:781309", 26, 98, null, null, 483368482, 520890813, 365891957, 296624399, 781309, "SRX9244925", "SRS7477618", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00026, 0.00325, 0.00019, 0.00021, 0.99995, 0.99691, 0.16666, 0.67331, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61443, "SRR12774413", "SRX9244924", "SRS7477617", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr20 scar", "GSM4817981", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr20 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817981", "GSM4817981: Injured heart Hr20 scar; Danio rerio; RNA Seq", "GSM4817981", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr20_30dpi_scar_R1.fastq.gz Hr20_30dpi_scar_R2.fastq.gz", "fastq fastq", 1734128220.0, 13984905.0, "GSM4817981 r1", "0:26 1:98", "A:504149488;C:546423208;G:375429746;T:307316098;N:809680", 26, 98, null, null, 504149488, 546423208, 375429746, 307316098, 809680, "SRX9244924", "SRS7477617", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00023, 0.00304, 0.00021, 0.00021, 0.99997, 0.99671, 0.0, 0.69251, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61444, "SRR12774412", "SRX9244923", "SRS7477616", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr19 scar", "GSM4817980", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr19 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817980", "GSM4817980: Injured heart Hr19 scar; Danio rerio; RNA Seq", "GSM4817980", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr19_30dpi_scar_R1.fastq.gz Hr19_30dpi_scar_R2.fastq.gz", "fastq fastq", 1709388732.0, 13785393.0, "GSM4817980 r1", "0:26 1:98", "A:497360883;C:535604667;G:371609960;T:304012638;N:800584", 26, 98, null, null, 497360883, 535604667, 371609960, 304012638, 800584, "SRX9244923", "SRS7477616", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.0, 0.00223, 0.0, 0.00015, 1.0, 0.99732, null, 0.68197, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61445, "SRR12774411", "SRX9244922", "SRS7477615", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr15 scar", "GSM4817979", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr15 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817979", "GSM4817979: Injured heart Hr15 scar; Danio rerio; RNA Seq", "GSM4817979", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817979", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr15_7dpi_scar_R1.fastq.gz Hr15_7dpi_scar_R2.fastq.gz", "fastq fastq", 2087880876.0, 16837749.0, "GSM4817979 r1", "0:26 1:98", "A:607249349;C:654858036;G:459453727;T:365342143;N:977621", 26, 98, null, null, 607249349, 654858036, 459453727, 365342143, 977621, "SRX9244922", "SRS7477615", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00049, 0.00233, 0.00047, 0.00019, 0.99993, 0.99762, 0.66666, 0.67844, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61446, "SRR12774410", "SRX9244921", "SRS7477614", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr14 scar", "GSM4817978", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr14 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817978", "GSM4817978: Injured heart Hr14 scar; Danio rerio; RNA Seq", "GSM4817978", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr14_7dpi_scar_R1.fastq.gz Hr14_7dpi_scar_R2.fastq.gz", "fastq fastq", 2347278956.0, 18929669.0, "GSM4817978 r1", "0:26 1:98", "A:681886627;C:738708862;G:506943538;T:418646627;N:1093302", 26, 98, null, null, 681886627, 738708862, 506943538, 418646627, 1093302, "SRX9244921", "SRS7477614", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00031, 0.00869, 0.00029, 0.00064, 0.99995, 0.99253, 1.0, 0.65963, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61447, "SRR12774385", "SRX9244920", "SRS7477613", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr29", "GSM4817956", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:IWR treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr29", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:IWR treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817956", "GSM4817956: Injured heart Hr29; Danio rerio; RNA Seq", "GSM4817956", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817956", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr29_3dpi_iwr1_R1.fastq.gz Hr29_3dpi_iwr1_R2.fastq.gz", "fastq fastq", 34463582364.0, 232862043.0, "GSM4817956 r1", "0:28 1:120", "A:9984789260;C:8104074480;G:7573244159;T:8793575297;N:7899168", 28, 120, null, null, 9984789260, 8104074480, 7573244159, 8793575297, 7899168, "SRX9244920", "SRS7477613", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00642, 0.93281, 0.00164, 0.02559, 0.99728, 0.93377, 0.63007, 0.90615, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61448, "SRR12774384", "SRX9244919", "SRS7477612", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr28", "GSM4817955", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:DMSO control|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr28", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:DMSO control|strain:Zebrabow M|10x chemistry version:v3", "GSM4817955", "GSM4817955: Injured heart Hr28; Danio rerio; RNA Seq", "GSM4817955", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817955", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr28_3dpi_dmso_R1.fastq.gz Hr28_3dpi_dmso_R2.fastq.gz", "fastq fastq", 47639345116.0, 321887467.0, "GSM4817955 r1", "0:28 1:120", "A:13409549383;C:11305025353;G:10522059988;T:12391822695;N:10887697", 28, 120, null, null, 13409549383, 11305025353, 10522059988, 12391822695, 10887697, "SRX9244919", "SRS7477612", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00891, 0.95539, 0.00273, 0.04532, 0.99612, 0.89167, 0.56462, 0.78131, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61449, "SRR12774383", "SRX9244918", "SRS7477611", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr27", "GSM4817954", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr27", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817954", "GSM4817954: Injured heart Hr27; Danio rerio; RNA Seq", "GSM4817954", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817954", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr27_3dpi_R1.fastq.gz Hr27_3dpi_R2.fastq.gz", "fastq fastq", 21969263264.0, 148440968.0, "GSM4817954 r1", "0:28 1:120", "A:6225612607;C:5049031461;G:4982110071;T:5687279874;N:25229251", 28, 120, null, null, 6225612607, 5049031461, 4982110071, 5687279874, 25229251, "SRX9244918", "SRS7477611", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.01407, 0.94367, 0.00467, 0.08768, 0.99186, 0.84078, 0.34541, 0.71335, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61450, "SRR12774382", "SRX9244917", "SRS7477610", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr26", "GSM4817953", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr26", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817953", "GSM4817953: Injured heart Hr26; Danio rerio; RNA Seq", "GSM4817953", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817953", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr26_3dpi_R1.fastq.gz Hr26_3dpi_R2.fastq.gz", "fastq fastq", 33427909296.0, 225864252.0, "GSM4817953 r1", "0:28 1:120", "A:9364593361;C:7730158729;G:7494192336;T:8800460968;N:38503902", 28, 120, null, null, 9364593361, 7730158729, 7494192336, 8800460968, 38503902, "SRX9244917", "SRS7477610", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00803, 0.95224, 0.0023, 0.07699, 0.99257, 0.83964, 0.42495, 0.69023, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61451, "SRR12774381", "SRX9244916", "SRS7477609", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr25", "GSM4817952", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr25", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817952", "GSM4817952: Injured heart Hr25; Danio rerio; RNA Seq", "GSM4817952", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817952", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr25_3dpi_R1.fastq.gz Hr25_3dpi_R2.fastq.gz", "fastq fastq", 31337707664.0, 211741268.0, "GSM4817952 r1", "0:28 1:120", "A:9203629209;C:7407902288;G:6671035692;T:8046939274;N:8201201", 28, 120, null, null, 9203629209, 7407902288, 6671035692, 8046939274, 8201201, "SRX9244916", "SRS7477609", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00806, 0.9436, 0.00224, 0.02177, 0.99719, 0.94412, 0.60127, 0.7944, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61452, "SRR12774380", "SRX9244915", "SRS7477608", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr24", "GSM4817951", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr24", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817951", "GSM4817951: Injured heart Hr24; Danio rerio; RNA Seq", "GSM4817951", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817951", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr24_3dpi_R1.fastq.gz Hr24_3dpi_R2.fastq.gz", "fastq fastq", 36097937040.0, 243904980.0, "GSM4817951 r1", "0:28 1:120", "A:9558730555;C:8754260918;G:8169609696;T:9605708114;N:9627757", 28, 120, null, null, 9558730555, 8754260918, 8169609696, 9605708114, 9627757, "SRX9244915", "SRS7477608", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00759, 0.97019, 0.00232, 0.04455, 0.99513, 0.88667, 0.44332, 0.62702, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61453, "SRR12774379", "SRX9244914", "SRS7477607", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr22", "GSM4817950", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "Injured heart Hr22", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v3", "GSM4817950", "GSM4817950: Injured heart Hr22; Danio rerio; RNA Seq", "GSM4817950", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817950", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr22_3dpi_R1.fastq.gz Hr22_3dpi_R2.fastq.gz", "fastq fastq", 30760517400.0, 222902300.0, "GSM4817950 r1", "0:28 1:110", "A:8456318022;C:7309256692;G:6808871738;T:8156929199;N:29141749", 28, 110, null, null, 8456318022, 7309256692, 6808871738, 8156929199, 29141749, "SRX9244914", "SRS7477607", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00623, 0.96798, 0.00179, 0.05265, 0.99525, 0.88487, 0.53684, 0.70915, 28, 110, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61454, "SRR12774378", "SRX9244913", "SRS7477606", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr21", "GSM4817949", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr21", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817949", "GSM4817949: Injured heart Hr21; Danio rerio; RNA Seq", "GSM4817949", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817949", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr21_30dpi_R1.fastq.gz Hr21_30dpi_R2.fastq.gz", "fastq fastq", 15355797796.0, 123837079.0, "GSM4817949 r1", "0:26 1:98", "A:4316318606;C:3764848972;G:3050050729;T:4217200184;N:7379305", 26, 98, null, null, 4316318606, 3764848972, 3050050729, 4217200184, 7379305, "SRX9244913", "SRS7477606", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.0011, 0.94795, 0.00027, 0.02366, 0.99886, 0.93371, 0.69753, 0.7893, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61455, "SRR12774377", "SRX9244912", "SRS7477605", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr20", "GSM4817948", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr20", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817948", "GSM4817948: Injured heart Hr20; Danio rerio; RNA Seq", "GSM4817948", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817948", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr20_30dpi_R1.fastq.gz Hr20_30dpi_R2.fastq.gz", "fastq fastq", 14225408960.0, 114721040.0, "GSM4817948 r1", "0:26 1:98", "A:4008435128;C:3473412702;G:2854957061;T:3881758456;N:6845613", 26, 98, null, null, 4008435128, 3473412702, 2854957061, 3881758456, 6845613, "SRX9244912", "SRS7477605", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00139, 0.95151, 0.00032, 0.02886, 0.9988, 0.92456, 0.66183, 0.77342, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61456, "SRR12774376", "SRX9244911", "SRS7477604", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr19", "GSM4817947", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr19", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:30|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817947", "GSM4817947: Injured heart Hr19; Danio rerio; RNA Seq", "GSM4817947", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817947", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr19_30dpi_R1.fastq.gz Hr19_30dpi_R2.fastq.gz", "fastq fastq", 15351522896.0, 123802604.0, "GSM4817947 r1", "0:26 1:98", "A:4281678414;C:3757866990;G:3159039093;T:4145577367;N:7361032", 26, 98, null, null, 4281678414, 3757866990, 3159039093, 4145577367, 7361032, "SRX9244911", "SRS7477604", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.0017, 0.95805, 0.00035, 0.02374, 0.99849, 0.92652, 0.65779, 0.68148, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61457, "SRR12774375", "SRX9244910", "SRS7477603", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr14", "GSM4817946", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr14", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817946", "GSM4817946: Injured heart Hr14; Danio rerio; RNA Seq", "GSM4817946", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817946", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr14_7dpi_R1.fastq.gz Hr14_7dpi_R2.fastq.gz", "fastq fastq", 22107805744.0, 178288756.0, "GSM4817946 r1", "0:26 1:98", "A:6166282241;C:5207350000;G:4841836144;T:5881754777;N:10582582", 26, 98, null, null, 6166282241, 5207350000, 4841836144, 5881754777, 10582582, "SRX9244910", "SRS7477603", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00217, 0.94044, 0.00067, 0.06845, 0.99671, 0.87533, 0.54639, 0.6124, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61458, "SRR12774374", "SRX9244909", "SRS7477602", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr13", "GSM4817945", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr13", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817945", "GSM4817945: Injured heart Hr13; Danio rerio; RNA Seq", "GSM4817945", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817945", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr13_7dpi_R1.fastq.gz Hr13_7dpi_R2.fastq.gz", "fastq fastq", 21988196832.0, 177324168.0, "GSM4817945 r1", "0:26 1:98", "A:6166548155;C:5130351133;G:4604715531;T:6076000631;N:10581382", 26, 98, null, null, 6166548155, 5130351133, 4604715531, 6076000631, 10581382, "SRX9244909", "SRS7477602", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00211, 0.93645, 0.00048, 0.08859, 0.99685, 0.86387, 0.58227, 0.65236, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61459, "SRR12774373", "SRX9244908", "SRS7477601", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr12", "GSM4817944", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr12", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817944", "GSM4817944: Injured heart Hr12; Danio rerio; RNA Seq", "GSM4817944", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817944", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr12_3dpi_R1.fastq.gz Hr12_3dpi_R2.fastq.gz", "fastq fastq", 28022423836.0, 225987289.0, "GSM4817944 r1", "0:26 1:98", "A:7791062679;C:6561427796;G:6229322338;T:7427193021;N:13418002", 26, 98, null, null, 7791062679, 6561427796, 6229322338, 7427193021, 13418002, "SRX9244908", "SRS7477601", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00322, 0.94469, 0.00082, 0.07604, 0.99433, 0.85865, 0.56929, 0.67126, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61460, "SRR12774372", "SRX9244907", "SRS7477600", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr10", "GSM4817943", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr10", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817943", "GSM4817943: Injured heart Hr10; Danio rerio; RNA Seq", "GSM4817943", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817943", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr10_3dpi_R1.fastq.gz Hr10_3dpi_R2.fastq.gz", "fastq fastq", 32806586754.0, 224702649.0, "GSM4817943 r1", "0:26 1:120", "A:9613897739;C:6920863013;G:7459564336;T:8784599303;N:27662363", 26, 120, null, null, 9613897739, 6920863013, 7459564336, 8784599303, 27662363, "SRX9244907", "SRS7477600", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00375, 0.91942, 0.00125, 0.13195, 0.99407, 0.86072, 0.42483, 0.61012, 26, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61461, "SRR12774371", "SRX9244906", "SRS7477599", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr9", "GSM4817942", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr9", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817942", "GSM4817942: Injured heart Hr9; Danio rerio; RNA Seq", "GSM4817942", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817942", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr9_7dpi_R1.fastq.gz Hr9_7dpi_R2.fastq.gz", "fastq fastq", 63316804040.0, 433676740.0, "GSM4817942 r1", "0:26 1:120", "A:18447552385;C:13622567490;G:14018738288;T:17207721498;N:20224379", 26, 120, null, null, 18447552385, 13622567490, 14018738288, 17207721498, 20224379, "SRX9244906", "SRS7477599", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00618, 0.93306, 0.00148, 0.11841, 0.99125, 0.90003, 0.36194, 0.5495, 26, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61462, "SRR12774370", "SRX9244905", "SRS7477598", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr7 Ventricle", "GSM4817941", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr7 Ventricle", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817941", "GSM4817941: Injured heart Hr7 Ventricle; Danio rerio; RNA Seq", "GSM4817941", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817941", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr7_7dpi_Ventricle_R1.fastq.gz Hr7_7dpi_Ventricle_R2.fastq.gz", "fastq fastq", 26688894024.0, 182800644.0, "GSM4817941 r1", "0:26 1:120", "A:7985425821;C:5821304405;G:5597449199;T:7280954252;N:3760347", 26, 120, null, null, 7985425821, 5821304405, 5597449199, 7280954252, 3760347, "SRX9244905", "SRS7477598", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00534, 0.94088, 0.00127, 0.1227, 0.99259, 0.91405, 0.38866, 0.6735, 26, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61463, "SRR12774409", "SRX9244904", "SRS7477597", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr13 scar", "GSM4817977", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr13 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817977", "GSM4817977: Injured heart Hr13 scar; Danio rerio; RNA Seq", "GSM4817977", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr13_7dpi_scar_R1.fastq.gz Hr13_7dpi_scar_R2.fastq.gz", "fastq fastq", 2236588000.0, 18037000.0, "GSM4817977 r1", "0:26 1:98", "A:648794902;C:704290257;G:486125037;T:396331832;N:1045972", 26, 98, null, null, 648794902, 704290257, 486125037, 396331832, 1045972, "SRX9244904", "SRS7477597", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00016, 0.00318, 0.00015, 0.00022, 0.99997, 0.9964, 1.0, 0.67407, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61464, "SRR12774408", "SRX9244903", "SRS7477596", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr12 scar", "GSM4817976", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr12 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817976", "GSM4817976: Injured heart Hr12 scar; Danio rerio; RNA Seq", "GSM4817976", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr12_3dpi_scar_R1.fastq.gz Hr12_3dpi_scar_R2.fastq.gz", "fastq fastq", 2442535508.0, 19697867.0, "GSM4817976 r1", "0:26 1:98", "A:708532406;C:760776372;G:527760418;T:444325003;N:1141309", 26, 98, null, null, 708532406, 760776372, 527760418, 444325003, 1141309, "SRX9244903", "SRS7477596", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00021, 0.0027, 0.00019, 0.00017, 0.99995, 0.99693, 0.5, 0.66569, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61465, "SRR12774407", "SRX9244902", "SRS7477595", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr11 scar", "GSM4817975", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr11 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817975", "GSM4817975: Injured heart Hr11 scar; Danio rerio; RNA Seq", "GSM4817975", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr11_3dpi_scar_R1.fastq.gz Hr11_3dpi_scar_R2.fastq.gz", "fastq fastq", 1668328364.0, 13454261.0, "GSM4817975 r1", "0:26 1:98", "A:480023159;C:527856459;G:363119451;T:296552327;N:776968", 26, 98, null, null, 480023159, 527856459, 363119451, 296552327, 776968, "SRX9244902", "SRS7477595", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00024, 0.00265, 0.00018, 0.00015, 0.99987, 0.99738, 0.77777, 0.69034, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61466, "SRR12774406", "SRX9244901", "SRS7477594", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "GEO accession GSM4817974 is currently private and is scheduled to be released on Jul 01 2022.", "GSM4817974", null, null, "Injured heart Hr10 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817974", "GSM4817974: Injured heart Hr10 scar; Danio rerio; RNA Seq", "GSM4817974", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817974", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr10_3dpi_scar_R1.fastq.gz Hr10_3dpi_scar_R2.fastq.gz", "fastq fastq", 2184983416.0, 17620834.0, "GSM4817974 r1", "0:26 1:98", "A:629594649;C:682046344;G:474913879;T:397410662;N:1017882", 26, 98, null, null, 629594649, 682046344, 474913879, 397410662, 1017882, "SRX9244901", "SRS7477594", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00016, 0.0028, 0.00014, 0.00027, 0.99993, 0.99687, 0.0, 0.69295, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [61467, "SRR12774404", "SRX9244900", "SRS7477593", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "GEO accession GSM4817973 is currently private and is scheduled to be released on Jul 01 2022.", "GSM4817973", null, null, "Injured heart Hr7 scar", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns \u201cCell\u201d \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:7|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817973", "GSM4817973: Injured heart Hr7 scar; Danio rerio; RNA Seq", "GSM4817973", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817973", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP286401", null, null, "Hr7_7dpi_Atrium_scar_R1.fastq.gz Hr7_7dpi_Atrium_scar_R2.fastq.gz", "fastq fastq", 2121897716.0, 14533546.0, "GSM4817973 r1", "0:26 1:120", "A:607542962;C:649120142;G:510713660;T:354236437;N:284515", 26, 120, null, null, 607542962, 649120142, 510713660, 354236437, 284515, "SRX9244900", "SRS7477593", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00021, 0.00509, 0.00016, 0.00014, 0.99993, 0.99965, 0.625, 0.29411, 26, 120, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "Heart", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 156, 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