{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\", experiment.library_strategy = \"RNA-Seq\" and technology = \"celseq\"", "rows": [[10060, "ERR4795364", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz", "fastq", 5410723202.0, 71707309.0, "E MTAB 9727:Sample 4", "0:75.46 1:0", "A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666", 75, 0, null, null, 1330416803, 531269504, 734031980, 2814959249, 45666, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.33614, null, 0.21532, null, 0.99019, null, 0.41002, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10061, "ERR4795365", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz", "fastq", 5414184547.0, 71707309.0, "E MTAB 9727:Sample 4 1", "0:0 1:75.50", "A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967", 0, 75, null, null, 1582938104, 1052565419, 1177180395, 1600161662, 1338967, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.84976, null, 0.28521, null, 0.85038, null, 0.5124, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10062, "ERR4795362", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz", "fastq", 4823193891.0, 63965519.0, "E MTAB 9727:Sample 3", "0:75.40 1:0", "A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086", 75, 0, null, null, 1323978162, 446831209, 581746343, 2470114091, 524086, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.36549, null, 0.19722, null, 0.95552, null, 0.4702, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10063, "ERR4795363", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz", "fastq", 4828889391.0, 63965519.0, "E MTAB 9727:Sample 3 1", "0:0 1:75.49", "A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756", 0, 75, null, null, 1434099697, 964508763, 893584575, 1534727600, 1968756, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.85811, null, 0.26231, null, 0.82731, null, 0.48618, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10064, "ERR4795360", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz", "fastq", 5598371393.0, 74235388.0, "E MTAB 9727:Sample 2", "0:75.41 1:0", "A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655", 75, 0, null, null, 1526486973, 558020193, 717587491, 2795646081, 630655, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.28059, null, 0.19252, null, 0.96404, null, 0.4874, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10065, "ERR4795361", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz", "fastq", 5600151371.0, 74235388.0, "E MTAB 9727:Sample 2 1", "0:0 1:75.44", "A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060", 0, 75, null, null, 1850568176, 1035622971, 1071138281, 1640475883, 2346060, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.7679, null, 0.30371, null, 0.82651, null, 0.43401, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10066, "ERR4795358", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz", "fastq", 4996502316.0, 66258508.0, "E MTAB 9727:Sample 1", "0:75.41 1:0", "A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936", 75, 0, null, null, 1330744174, 451622042, 591151500, 2622422664, 561936, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.29754, null, 0.17671, null, 0.9669, null, 0.45463, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10067, "ERR4795359", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz", "fastq", 4999908389.0, 66258508.0, "E MTAB 9727:Sample 1 1", "0:0 1:75.46", "A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512", 0, 75, null, null, 1591945117, 933968124, 986108614, 1485824022, 2062512, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.81333, null, 0.2466, null, 0.83027, null, 0.51572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25228, "SRR25685572", "SRX21410761", "SRS18649243", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart3", "GSM7717530", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi", "GSM7717530", "GSM7717530: zebrafish 14dpi heart3; Danio rerio; RNA Seq", "GSM7717530 r1", "GSM7717530", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "DB14zf4_R1.fq DB14zf4_R2.fq", "fastq fastq", 571157496.0, 7312520.0, "GSM7717530 r1", null, "A:132329616;C:53169305;G:72431948;T:313058610;N:168017", null, null, null, null, 132329616, 53169305, 72431948, 313058610, 168017, "SRX21410761", "SRS18649243", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.01414, 0.679, 0.01413, 0.08289, 1.0, 0.98395, null, 0.48915, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25229, "SRR25685573", "SRX21410760", "SRS18649241", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart2", "GSM7717529", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi", "GSM7717529", "GSM7717529: zebrafish 14dpi heart2; Danio rerio; RNA Seq", "GSM7717529 r1", "GSM7717529", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "DB14zf3_R1.fq DB14zf3_R2.fq", "fastq fastq", 97890367.0, 1292037.0, "GSM7717529 r1", null, "A:21637243;C:8563955;G:12004508;T:55662880;N:21781", null, null, null, null, 21637243, 8563955, 12004508, 55662880, 21781, "SRX21410760", "SRS18649241", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.0, 0.689, 0.0, 0.07655, 1.0, 0.99831, null, 0.63709, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25230, "SRR25685574", "SRX21410759", "SRS18649242", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart1", "GSM7717528", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi", "GSM7717528", "GSM7717528: zebrafish 14dpi heart1; Danio rerio; RNA Seq", "GSM7717528 r1", "GSM7717528", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "DB14zf1_R1.fq DB14zf1_R2.fq", "fastq fastq", 1031757474.0, 7257847.0, "GSM7717528 r1", null, "A:276216587;C:146620316;G:184052670;T:423474577;N:1393324", null, null, null, null, 276216587, 146620316, 184052670, 423474577, 1393324, "SRX21410759", "SRS18649242", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.04176, 0.6198, 0.03023, 0.08234, 0.99894, 0.88885, 0.64556, 0.53126, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25231, "SRR25685575", "SRX21410758", "SRS18649240", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart3", "GSM7717527", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717527", "GSM7717527: zebrafish 7dpi heart3; Danio rerio; RNA Seq", "GSM7717527 r1", "GSM7717527", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "D37DPIZF3_R1.fq D37DPIZF3_R2.fq", "fastq fastq", 898901460.0, 7585924.0, "GSM7717527 r1", null, "A:236935836;C:100995680;G:128458892;T:431620821;N:890231", null, null, null, null, 236935836, 100995680, 128458892, 431620821, 890231, "SRX21410758", "SRS18649240", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.12082, 0.70068, 0.10594, 0.1234, 0.99983, 0.90136, 0.875, 0.48346, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25232, "SRR25685576", "SRX21410757", "SRS18649239", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart2", "GSM7717526", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717526", "GSM7717526: zebrafish 7dpi heart2; Danio rerio; RNA Seq", "GSM7717526 r1", "GSM7717526", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "D27DPIZF2_R1.fq D27DPIZF2_R2.fq", "fastq fastq", 1060429257.0, 7609110.0, "GSM7717526 r1", null, "A:283107752;C:130181128;G:159305328;T:486464477;N:1370572", null, null, null, null, 283107752, 130181128, 159305328, 486464477, 1370572, "SRX21410757", "SRS18649239", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.19472, 0.68783, 0.17584, 0.16739, 0.99967, 0.85628, 0.44, 0.56319, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25233, "SRR25685577", "SRX21410756", "SRS18649238", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart1", "GSM7717525", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717525", "GSM7717525: zebrafish 7dpi heart1; Danio rerio; RNA Seq", "GSM7717525 r1", "GSM7717525", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options: allowEarlyFileEnd", "D17DPIZF1_R1.fq D17DPIZF1_R2.fq", "fastq fastq", 1073044507.0, 7624815.0, "GSM7717525 r1", null, "A:288576038;C:136858647;G:170330711;T:475869519;N:1409592", null, null, null, null, 288576038, 136858647, 170330711, 475869519, 1409592, "SRX21410756", "SRS18649238", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.15938, 0.70435, 0.14583, 0.08079, 0.99981, 0.87949, 0.38461, 0.57027, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25234, "SRR25685578", "SRX21410755", "SRS18649237", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart3", "GSM7717524", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717524", "GSM7717524: zebrafish 3dpi heart3; Danio rerio; RNA Seq", "GSM7717524 r1", "GSM7717524", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART3_R1.fastq FKHEART3_R2.fastq", "fastq fastq", 781079621.0, 5184230.0, "GSM7717524 r1", "0:75.26 1:75.40", "A:277491111;C:118539142;G:116911958;T:268048500;N:88910", 75, 75, null, null, 277491111, 118539142, 116911958, 268048500, 88910, "SRX21410755", "SRS18649237", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.04348, 0.71869, 0.04347, 0.28823, 1.0, 0.79681, null, 0.53909, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25235, "SRR25685579", "SRX21410754", "SRS18649236", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart2", "GSM7717523", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717523", "GSM7717523: zebrafish 3dpi heart2; Danio rerio; RNA Seq", "GSM7717523 r1", "GSM7717523", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART2_R1.fastq FKHEART2_R2.fastq", "fastq fastq", 684820059.0, 4547520.0, "GSM7717523 r1", "0:75.21 1:75.38", "A:258487418;C:93776953;G:97187917;T:235293267;N:74504", 75, 75, null, null, 258487418, 93776953, 97187917, 235293267, 74504, "SRX21410754", "SRS18649236", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09406, 0.79542, 0.09405, 0.0802, 1.0, 0.83029, null, 0.56367, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25236, "SRR25685580", "SRX21410753", "SRS18649235", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart1", "GSM7717522", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717522", "GSM7717522: zebrafish 3dpi heart1; Danio rerio; RNA Seq", "GSM7717522 r1", "GSM7717522", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART1_R1.fastq FKHEART1_R2.fastq", "fastq fastq", 784558404.0, 5209213.0, "GSM7717522 r1", "0:75.22 1:75.39", "A:291009319;C:102718146;G:111606154;T:279144074;N:80711", 75, 75, null, null, 291009319, 102718146, 111606154, 279144074, 80711, "SRX21410753", "SRS18649235", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.13119, 0.82035, 0.12871, 0.08445, 0.99997, 0.82785, 0.0, 0.56254, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25239, "SRR25723792", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz", "fastq fastq", 529790530.0, 6160355.0, "GSM7728123 r1", "0:26 1:60", "A:134254092;C:100685793;G:108463112;T:186279563;N:107970", 26, 60, null, null, 134254092, 100685793, 108463112, 186279563, 107970, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11277, 0.80912, 0.10457, 0.43275, 0.99131, 0.93933, 0.67026, 0.54274, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25240, "SRR25723793", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L002_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L002_R2_001.fastq.gz", "fastq fastq", 611015122.0, 7104827.0, "GSM7728123 r2", "0:26 1:60", "A:152137832;C:116026517;G:127735448;T:214967198;N:148127", 26, 60, null, null, 152137832, 116026517, 127735448, 214967198, 148127, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11413, 0.81785, 0.10565, 0.44205, 0.99119, 0.93419, 0.59743, 0.53882, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25241, "SRR25723794", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz", "fastq fastq", 554981822.0, 6453277.0, "GSM7728123 r3", "0:26 1:60", "A:140664360;C:105281601;G:113575873;T:195359632;N:100356", 26, 60, null, null, 140664360, 105281601, 113575873, 195359632, 100356, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11352, 0.80651, 0.10538, 0.42971, 0.99137, 0.93994, 0.65893, 0.53098, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25242, "SRR25723795", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz", "fastq fastq", 459861436.0, 5347226.0, "GSM7728123 r4", "0:26 1:60", "A:115949245;C:86913961;G:95720860;T:161187969;N:89401", 26, 60, null, null, 115949245, 86913961, 95720860, 161187969, 89401, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11249, 0.81109, 0.10407, 0.43334, 0.99135, 0.94034, 0.64852, 0.53864, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25243, "SRR25723796", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L001_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L001_R2_001.fastq.gz", "fastq fastq", 584059454.0, 6791389.0, "GSM7728122 r1", "0:26 1:60", "A:162038298;C:107975394;G:118251259;T:195669218;N:125285", 26, 60, null, null, 162038298, 107975394, 118251259, 195669218, 125285, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.08872, 0.68673, 0.08328, 0.37858, 0.99346, 0.94945, 0.60282, 0.42608, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25244, "SRR25723797", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L002_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L002_R2_001.fastq.gz", "fastq fastq", 641359448.0, 7457668.0, "GSM7728122 r2", "0:26 1:60", "A:174443468;C:118438230;G:132604485;T:215721538;N:151727", 26, 60, null, null, 174443468, 118438230, 132604485, 215721538, 151727, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09277, 0.71427, 0.08722, 0.3942, 0.99338, 0.94594, 0.56903, 0.45872, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25245, "SRR25723798", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L003_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L003_R2_001.fastq.gz", "fastq fastq", 609857046.0, 7091361.0, "GSM7728122 r3", "0:26 1:60", "A:169007241;C:112556048;G:123345017;T:204831635;N:117105", 26, 60, null, null, 169007241, 112556048, 123345017, 204831635, 117105, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09058, 0.68251, 0.08521, 0.37718, 0.99332, 0.95156, 0.59403, 0.44605, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25246, "SRR25723799", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L004_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L004_R2_001.fastq.gz", "fastq fastq", 514759966.0, 5985581.0, "GSM7728122 r4", "0:26 1:60", "A:142060859;C:94579961;G:106100208;T:171916257;N:102681", 26, 60, null, null, 142060859, 94579961, 106100208, 171916257, 102681, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.08962, 0.7176, 0.08411, 0.39394, 0.99293, 0.95189, 0.55398, 0.46149, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25247, "SRR25723800", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz", "fastq fastq", 929999528.0, 10813948.0, "GSM7728121 r1", "0:26 1:60", "A:240334465;C:174255952;G:184260587;T:330943403;N:205121", 26, 60, null, null, 240334465, 174255952, 184260587, 330943403, 205121, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11113, 0.87407, 0.10304, 0.43976, 0.992, 0.93034, 0.63031, 0.44624, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25248, "SRR25723801", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz", "fastq fastq", 987824896.0, 11486336.0, "GSM7728121 r2", "0:26 1:60", "A:251121714;C:184449811;G:201317783;T:350692225;N:243363", 26, 60, null, null, 251121714, 184449811, 201317783, 350692225, 243363, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11267, 0.87874, 0.10429, 0.4457, 0.99184, 0.92498, 0.56612, 0.45489, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25249, "SRR25723802", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz", "fastq fastq", 959933032.0, 11162012.0, "GSM7728121 r3", "0:26 1:60", "A:247983556;C:179564753;G:190342582;T:341858456;N:183685", 26, 60, null, null, 247983556, 179564753, 190342582, 341858456, 183685, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.1118, 0.87156, 0.10348, 0.43983, 0.99149, 0.93034, 0.65287, 0.44548, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25250, "SRR25723803", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz", "fastq fastq", 798370766.0, 9283381.0, "GSM7728121 r4", "0:26 1:60", "A:205538880;C:148510556;G:161196381;T:282964175;N:160774", 26, 60, null, null, 205538880, 148510556, 161196381, 282964175, 160774, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11018, 0.87017, 0.10214, 0.43625, 0.99226, 0.93332, 0.56058, 0.44211, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25251, "SRR25723804", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz", "fastq fastq", 806178534.0, 9374169.0, "GSM7728120 r1", "0:26 1:60", "A:213590554;C:148614157;G:163804315;T:279996916;N:172592", 26, 60, null, null, 213590554, 148614157, 163804315, 279996916, 172592, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10778, 0.79219, 0.10092, 0.39443, 0.99255, 0.93712, 0.64412, 0.39504, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25252, "SRR25723805", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz", "fastq fastq", 874594286.0, 10169701.0, "GSM7728120 r2", "0:26 1:60", "A:227213153;C:160851586;G:182364146;T:303951184;N:214217", 26, 60, null, null, 227213153, 160851586, 182364146, 303951184, 214217, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11064, 0.80317, 0.1038, 0.40093, 0.99249, 0.9332, 0.652, 0.40914, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25253, "SRR25723806", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz", "fastq fastq", 831835860.0, 9672510.0, "GSM7728120 r3", "0:26 1:60", "A:220300204;C:153061412;G:168938657;T:289375449;N:160138", 26, 60, null, null, 220300204, 153061412, 168938657, 289375449, 160138, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10987, 0.78665, 0.10348, 0.39264, 0.99316, 0.93661, 0.66753, 0.37676, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25254, "SRR25723807", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz", "fastq fastq", 692573136.0, 8053176.0, "GSM7728120 r4", "0:26 1:60", "A:182418113;C:126757471;G:143869511;T:239393143;N:134898", 26, 60, null, null, 182418113, 126757471, 143869511, 239393143, 134898, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10825, 0.81365, 0.10178, 0.40513, 0.99308, 0.94032, 0.67299, 0.41125, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25255, "SRR25723808", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L001_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L001_R2_001.fastq.gz", "fastq fastq", 364147736.0, 4234276.0, "GSM7728119 r1", "0:26 1:60", "A:94538754;C:69024492;G:68361658;T:132108181;N:114651", 26, 60, null, null, 94538754, 69024492, 68361658, 132108181, 114651, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11558, 0.78278, 0.10659, 0.24226, 0.9893, 0.92719, 0.58692, 0.48105, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25256, "SRR25723809", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L002_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L002_R2_001.fastq.gz", "fastq fastq", 377653262.0, 4391317.0, "GSM7728119 r2", "0:26 1:60", "A:99999342;C:71104204;G:70005970;T:136434888;N:108858", 26, 60, null, null, 99999342, 71104204, 70005970, 136434888, 108858, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11405, 0.77996, 0.10525, 0.24008, 0.98963, 0.93616, 0.60855, 0.44129, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25257, "SRR25723810", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L003_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L003_R2_001.fastq.gz", "fastq fastq", 306947588.0, 3569158.0, "GSM7728119 r3", "0:26 1:60", "A:80261116;C:58220837;G:57196503;T:111195958;N:73174", 26, 60, null, null, 80261116, 58220837, 57196503, 111195958, 73174, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11141, 0.76713, 0.10254, 0.23772, 0.98938, 0.93314, 0.62261, 0.47885, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25258, "SRR25723811", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L004_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L004_R2_001.fastq.gz", "fastq fastq", 389472414.0, 4528749.0, "GSM7728119 r4", "0:26 1:60", "A:102486709;C:73105388;G:73019179;T:140769931;N:91207", 26, 60, null, null, 102486709, 73105388, 73019179, 140769931, 91207, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11502, 0.78307, 0.10673, 0.24219, 0.98967, 0.93308, 0.64527, 0.43659, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25259, "SRR25723812", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L001_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L001_R2_001.fastq.gz", "fastq fastq", 381365624.0, 4434484.0, "GSM7728118 r1", "0:26 1:60", "A:102130758;C:71032768;G:73641442;T:134437630;N:123026", 26, 60, null, null, 102130758, 71032768, 73641442, 134437630, 123026, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10052, 0.7243, 0.09214, 0.25633, 0.9892, 0.92985, 0.52345, 0.5112, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25260, "SRR25723813", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L002_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L002_R2_001.fastq.gz", "fastq fastq", 400525220.0, 4657270.0, "GSM7728118 r2", "0:26 1:60", "A:109307778;C:73934198;G:76916762;T:140249156;N:117326", 26, 60, null, null, 109307778, 73934198, 76916762, 140249156, 117326, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09923, 0.71601, 0.09078, 0.25139, 0.98948, 0.93914, 0.52314, 0.5078, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25261, "SRR25723814", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L003_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L003_R2_001.fastq.gz", "fastq fastq", 341364014.0, 3969349.0, "GSM7728118 r3", "0:26 1:60", "A:91716565;C:63676514;G:65563102;T:120323617;N:84216", 26, 60, null, null, 91716565, 63676514, 65563102, 120323617, 84216, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09826, 0.7079, 0.09008, 0.2497, 0.98918, 0.93809, 0.52649, 0.49781, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25262, "SRR25723815", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L004_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L004_R2_001.fastq.gz", "fastq fastq", 414000732.0, 4813962.0, "GSM7728118 r4", "0:26 1:60", "A:112224009;C:76213738;G:80259829;T:145201785;N:101371", 26, 60, null, null, 112224009, 76213738, 80259829, 145201785, 101371, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10103, 0.71981, 0.09294, 0.25413, 0.98902, 0.93669, 0.52994, 0.51172, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25263, "SRR25723816", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz", "fastq fastq", 471703034.0, 5484919.0, "GSM7728117 r1", "0:26 1:60", "A:125045012;C:89627491;G:85413855;T:171466861;N:149815", 26, 60, null, null, 125045012, 89627491, 85413855, 171466861, 149815, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10906, 0.68002, 0.10212, 0.30506, 0.99101, 0.94219, 0.63738, 0.45862, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25264, "SRR25723817", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz", "fastq fastq", 489372938.0, 5690383.0, "GSM7728117 r2", "0:26 1:60", "A:131516821;C:92202683;G:88685608;T:176824985;N:142841", 26, 60, null, null, 131516821, 92202683, 88685608, 176824985, 142841, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11042, 0.68086, 0.10299, 0.30411, 0.99093, 0.94856, 0.60224, 0.46578, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25265, "SRR25723818", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz", "fastq fastq", 407735288.0, 4741108.0, "GSM7728117 r3", "0:26 1:60", "A:108841476;C:77418215;G:73171345;T:148203998;N:100254", 26, 60, null, null, 108841476, 77418215, 73171345, 148203998, 100254, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10882, 0.67068, 0.10177, 0.29557, 0.99151, 0.94686, 0.65762, 0.42658, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25266, "SRR25723819", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz", "fastq fastq", 505539304.0, 5878364.0, "GSM7728117 r4", "0:26 1:60", "A:135189083;C:94908231;G:92431583;T:182885125;N:125282", 26, 60, null, null, 135189083, 94908231, 92431583, 182885125, 125282, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10989, 0.68603, 0.10286, 0.30542, 0.99107, 0.94777, 0.65338, 0.42121, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [71397, "SRR21571181", "SRX17573445", "SRS15113179", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 2 GFP+ #3", "GSM6580971", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 2 GFP+ #3", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580971", "GSM6580971: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3; Danio rerio; RNA Seq", "GSM6580971 r1", "GSM6580971", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s014.R1.fastq.gz HAR-HN-s014.R2.fastq.gz", "fastq fastq", 2393526200.0, 27831700.0, "GSM6580971 r1", "0:26 1:60", "A:587629810;C:436040251;G:440163052;T:929430783;N:262304", 26, 60, null, null, 587629810, 436040251, 440163052, 929430783, 262304, "SRX17573445", "SRS15113179", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.1102, 0.89036, 0.10359, 0.25006, 0.99285, 0.81172, 0.56209, 0.58312, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71398, "SRR21571182", "SRX17573444", "SRS15113178", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+", "GSM6580970", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+", "GSM6580970", "GSM6580970: TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+; Danio rerio; RNA Seq", "GSM6580970 r1", "GSM6580970", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s013.R1.fastq.gz HAR-HN-s013.R2.fastq.gz", "fastq fastq", 2799404318.0, 32551213.0, "GSM6580970 r1", "0:26 1:60", "A:674562015;C:518279489;G:507732521;T:1093251404;N:5578889", 26, 60, null, null, 674562015, 518279489, 507732521, 1093251404, 5578889, "SRX17573444", "SRS15113178", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11385, 0.89818, 0.10608, 0.24805, 0.99162, 0.80519, 0.57833, 0.58452, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71399, "SRR21571183", "SRX17573443", "SRS15113177", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 2 GFP+ #2", "GSM6580969", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 2 GFP+ #2", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580969", "GSM6580969: TIE:EGFP MCR:MCS Tumor 2 GFP+ #2; Danio rerio; RNA Seq", "GSM6580969 r1", "GSM6580969", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s012.R1.fastq.gz HAR-HN-s012.R2.fastq.gz", "fastq fastq", 2643515042.0, 30738547.0, "GSM6580969 r1", "0:26 1:60", "A:644064543;C:487933120;G:466421088;T:1039827853;N:5268438", 26, 60, null, null, 644064543, 487933120, 466421088, 1039827853, 5268438, "SRX17573443", "SRS15113177", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11114, 0.8924, 0.10417, 0.25808, 0.99151, 0.80499, 0.60121, 0.567, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71400, "SRR21571184", "SRX17573442", "SRS15113176", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 2 GFP+ #1", "GSM6580968", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 2 GFP+ #1", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580968", "GSM6580968: TIE:EGFP MCR:MCS Tumor 2 GFP+ #1; Danio rerio; RNA Seq", "GSM6580968 r1", "GSM6580968", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s011.R1.fastq.gz HAR-HN-s011.R2.fastq.gz", "fastq fastq", 2701784858.0, 31416103.0, "GSM6580968 r1", "0:26 1:60", "A:654129800;C:498352764;G:495215316;T:1048678271;N:5408707", 26, 60, null, null, 654129800, 498352764, 495215316, 1048678271, 5408707, "SRX17573442", "SRS15113176", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.10435, 0.89555, 0.0971, 0.26327, 0.99354, 0.80647, 0.56789, 0.50648, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71401, "SRR21571185", "SRX17573441", "SRS15113175", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3", "GSM6580967", null, "source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:SATB2 Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580967", "GSM6580967: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3; Danio rerio; RNA Seq", "GSM6580967 r1", "GSM6580967", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s007.R1.fastq.gz HAR-HN-s007.R2.fastq.gz", "fastq fastq", 3169503770.0, 36854695.0, "GSM6580967 r1", "0:26 1:60", "A:758395203;C:580012810;G:565741250;T:1265023729;N:330778", 26, 60, null, null, 758395203, 580012810, 565741250, 1265023729, 330778, "SRX17573441", "SRS15113175", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11903, 0.89395, 0.11159, 0.29218, 0.99243, 0.79705, 0.54327, 0.56983, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71402, "SRR21571186", "SRX17573440", "SRS15113174", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+", "GSM6580966", null, "source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:SATB2 Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+", "GSM6580966", "GSM6580966: TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+; Danio rerio; RNA Seq", "GSM6580966 r1", "GSM6580966", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s006.R1.fastq.gz HAR-HN-s006.R2.fastq.gz", "fastq fastq", 3401223030.0, 39549105.0, "GSM6580966 r1", "0:26 1:60", "A:811721089;C:634467013;G:610447766;T:1344233621;N:353541", 26, 60, null, null, 811721089, 634467013, 610447766, 1344233621, 353541, "SRX17573440", "SRS15113174", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11728, 0.9042, 0.11084, 0.22711, 0.9931, 0.79494, 0.65306, 0.56756, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71403, "SRR21571187", "SRX17573439", "SRS15113173", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2", "GSM6580965", null, "source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:SATB2 Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580965", "GSM6580965: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2; Danio rerio; RNA Seq", "GSM6580965 r1", "GSM6580965", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s005.R1.fastq.gz HAR-HN-s005.R2.fastq.gz", "fastq fastq", 3042431718.0, 35377113.0, "GSM6580965 r1", "0:26 1:60", "A:744782141;C:565144430;G:541953297;T:1190237432;N:314418", 26, 60, null, null, 744782141, 565144430, 541953297, 1190237432, 314418, "SRX17573439", "SRS15113173", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11149, 0.88671, 0.10471, 0.23988, 0.99162, 0.79543, 0.64395, 0.58192, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71404, "SRR21571188", "SRX17573438", "SRS15113172", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1", "GSM6580964", null, "source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:SATB2 Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580964", "GSM6580964: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1; Danio rerio; RNA Seq", "GSM6580964 r1", "GSM6580964", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-HN-s004.R1.fastq.gz HAR-HN-s004.R2.fastq.gz", "fastq fastq", 3454727328.0, 40171248.0, "GSM6580964 r1", "0:26 1:60", "A:823342460;C:630914117;G:615200919;T:1384911330;N:358502", 26, 60, null, null, 823342460, 630914117, 615200919, 1384911330, 358502, "SRX17573438", "SRS15113172", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.12493, 0.8892, 0.11706, 0.21947, 0.99314, 0.79216, 0.73215, 0.53614, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71405, "SRR21571189", "SRX17573437", "SRS15113171", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 1 GFP+ #3", "GSM6580963", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 1 GFP+ #3", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580963", "GSM6580963: TIE:EGFP MCR:MCS Tumor 1 GFP+ #3; Danio rerio; RNA Seq", "GSM6580963 r1", "GSM6580963", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-SW-s016.R1.fastq.gz HAR-SW-s016.R2.fastq.gz", "fastq fastq", 2986527160.0, 34727060.0, "GSM6580963 r1", "0:26 1:60", "A:741435297;C:548375629;G:534147329;T:1162130158;N:438747", 26, 60, null, null, 741435297, 548375629, 534147329, 1162130158, 438747, "SRX17573437", "SRS15113171", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.12032, 0.87963, 0.11182, 0.30887, 0.99145, 0.79926, 0.53199, 0.59453, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71406, "SRR21571190", "SRX17573436", "SRS15113170", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ", "GSM6580962", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:mCherry+;GFP |geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:mCherry+;GFP ", "GSM6580962", "GSM6580962: TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ; Danio rerio; RNA Seq", "GSM6580962 r1", "GSM6580962", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-SW-s015.R1.fastq.gz HAR-SW-s015.R2.fastq.gz", "fastq fastq", 2668318990.0, 31026965.0, "GSM6580962 r1", "0:26 1:60", "A:650521761;C:486885070;G:465311971;T:1065210518;N:389670", 26, 60, null, null, 650521761, 486885070, 465311971, 1065210518, 389670, "SRX17573436", "SRS15113170", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.1142, 0.88526, 0.10718, 0.34648, 0.99198, 0.80428, 0.56024, 0.56437, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71407, "SRR21571191", "SRX17573435", "SRS15113168", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 1 GFP+ #2", "GSM6580961", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 1 GFP+ #2", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580961", "GSM6580961: TIE:EGFP MCR:MCS Tumor 1 GFP+ #2; Danio rerio; RNA Seq", "GSM6580961 r1", "GSM6580961", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-SW-s014.R1.fastq.gz HAR-SW-s014.R2.fastq.gz", "fastq fastq", 2393946138.0, 27836583.0, "GSM6580961 r1", "0:26 1:60", "A:596410784;C:437801560;G:418907527;T:940499589;N:326678", 26, 60, null, null, 596410784, 437801560, 418907527, 940499589, 326678, "SRX17573435", "SRS15113168", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.12342, 0.85959, 0.11689, 0.34528, 0.98965, 0.80472, 0.49199, 0.56661, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [71408, "SRR21571192", "SRX17573434", "SRS15113169", "SRP397130", "PRJNA880596", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]", "GSE213359", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed", "parent bioproject:PRJNA880593", null, null, "TIE:EGFP MCR:MCS Tumor 1 GFP+ #1", "GSM6580960", null, "source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing", "TIE:EGFP MCR:MCS Tumor 1 GFP+ #1", "The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv", "MCR:MCS Melanoma", "Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", "N/A", "tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+", "GSM6580960", "GSM6580960: TIE:EGFP MCR:MCS Tumor 1 GFP+ #1; Danio rerio; RNA Seq", "GSM6580960 r1", "GSM6580960", "1", "Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40\u00b5m filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP397130", null, null, "HAR-SW-s013.R1.fastq.gz HAR-SW-s013.R2.fastq.gz", "fastq fastq", 3043161084.0, 35385594.0, "GSM6580960 r1", "0:26 1:60", "A:750431276;C:555809857;G:537628053;T:1198847837;N:444061", 26, 60, null, null, 750431276, 555809857, 537628053, 1198847837, 444061, "SRX17573434", "SRS15113169", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11034, 0.86528, 0.10371, 0.32665, 0.99198, 0.79695, 0.51927, 0.58318, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [73951, "SRR23290994", "SRX19234275", "SRS16638733", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 2", "GSM7016815", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016815", "GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq", "GSM7016815 r1", "GSM7016815", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s041_H7L35BGXM_S4_L001_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L001_R2_001.fastq.gz", "fastq fastq", 858173876.0, 9978766.0, "GSM7016815 r1", "0:26 1:60", "A:213059809;C:160771814;G:156105199;T:328218073;N:18981", 26, 60, null, null, 213059809, 160771814, 156105199, 328218073, 18981, "SRX19234275", "SRS16638733", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11426, 0.88222, 0.10668, 0.29657, 0.99149, 0.8355, 0.60863, 0.67263, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73952, "SRR23290995", "SRX19234275", "SRS16638733", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 2", "GSM7016815", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016815", "GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq", "GSM7016815 r1", "GSM7016815", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s041_H7L35BGXM_S4_L002_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L002_R2_001.fastq.gz", "fastq fastq", 843721318.0, 9810713.0, "GSM7016815 r2", "0:26 1:60", "A:208714473;C:157371099;G:155893107;T:321724427;N:18212", 26, 60, null, null, 208714473, 157371099, 155893107, 321724427, 18212, "SRX19234275", "SRS16638733", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11232, 0.8799, 0.10497, 0.29809, 0.99123, 0.83621, 0.66836, 0.66521, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73953, "SRR23290996", "SRX19234275", "SRS16638733", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 2", "GSM7016815", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016815", "GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq", "GSM7016815 r1", "GSM7016815", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s041_H7L35BGXM_S4_L003_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L003_R2_001.fastq.gz", "fastq fastq", 864128860.0, 10048010.0, "GSM7016815 r3", "0:26 1:60", "A:214256028;C:161957471;G:157308166;T:330585259;N:21936", 26, 60, null, null, 214256028, 161957471, 157308166, 330585259, 21936, "SRX19234275", "SRS16638733", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.1147, 0.88514, 0.10704, 0.29827, 0.99105, 0.83321, 0.67314, 0.65637, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73954, "SRR23290997", "SRX19234275", "SRS16638733", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 2", "GSM7016815", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016815", "GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq", "GSM7016815 r1", "GSM7016815", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s041_H7L35BGXM_S4_L004_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L004_R2_001.fastq.gz", "fastq fastq", 862094960.0, 10024360.0, "GSM7016815 r4", "0:26 1:60", "A:212975380;C:160923939;G:159237695;T:328939876;N:18070", 26, 60, null, null, 212975380, 160923939, 159237695, 328939876, 18070, "SRX19234275", "SRS16638733", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11191, 0.88105, 0.10467, 0.2945, 0.99151, 0.83623, 0.67428, 0.67156, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73955, "SRR23290998", "SRX19234274", "SRS16638732", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 4", "GSM7016814", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 4", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016814", "GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq", "GSM7016814 r1", "GSM7016814", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s039_H7L35BGXM_S3_L001_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L001_R2_001.fastq.gz", "fastq fastq", 839750096.0, 9764536.0, "GSM7016814 r1", "0:26 1:60", "A:207245393;C:152642612;G:152075698;T:327767742;N:18651", 26, 60, null, null, 207245393, 152642612, 152075698, 327767742, 18651, "SRX19234274", "SRS16638732", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10807, 0.88063, 0.1011, 0.31218, 0.99133, 0.81844, 0.57963, 0.58371, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73956, "SRR23290999", "SRX19234274", "SRS16638732", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 4", "GSM7016814", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 4", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016814", "GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq", "GSM7016814 r1", "GSM7016814", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s039_H7L35BGXM_S3_L002_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L002_R2_001.fastq.gz", "fastq fastq", 824555530.0, 9587855.0, "GSM7016814 r2", "0:26 1:60", "A:202762477;C:149247401;G:151695233;T:320832302;N:18117", 26, 60, null, null, 202762477, 149247401, 151695233, 320832302, 18117, "SRX19234274", "SRS16638732", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10764, 0.87478, 0.1005, 0.31049, 0.99101, 0.81929, 0.58127, 0.51321, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73957, "SRR23291000", "SRX19234274", "SRS16638732", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 4", "GSM7016814", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 4", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016814", "GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq", "GSM7016814 r1", "GSM7016814", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s039_H7L35BGXM_S3_L003_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L003_R2_001.fastq.gz", "fastq fastq", 845111766.0, 9826881.0, "GSM7016814 r3", "0:26 1:60", "A:208286833;C:153694024;G:153159692;T:329951816;N:19401", 26, 60, null, null, 208286833, 153694024, 153159692, 329951816, 19401, "SRX19234274", "SRS16638732", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.1087, 0.88111, 0.10148, 0.31291, 0.99068, 0.81698, 0.55014, 0.58727, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73958, "SRR23291001", "SRX19234274", "SRS16638732", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 4", "GSM7016814", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 4", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016814", "GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq", "GSM7016814 r1", "GSM7016814", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-s039_H7L35BGXM_S3_L004_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L004_R2_001.fastq.gz", "fastq fastq", 842710216.0, 9798956.0, "GSM7016814 r4", "0:26 1:60", "A:206896294;C:152644705;G:155014140;T:328138108;N:16969", 26, 60, null, null, 206896294, 152644705, 155014140, 328138108, 16969, "SRX19234274", "SRS16638732", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10766, 0.87731, 0.10058, 0.31053, 0.99119, 0.81781, 0.57185, 0.57715, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73959, "SRR23291002", "SRX19234273", "SRS16638731", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 1", "GSM7016813", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016813", "GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq", "GSM7016813 r1", "GSM7016813", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-025_HCMYKBGXC_S8_L001_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L001_R2_001.fastq.gz", "fastq fastq", 638322358.0, 7422353.0, "GSM7016813 r1", "0:26 1:60", "A:152993677;C:129279491;G:116490423;T:238075133;N:1483634", 26, 60, null, null, 152993677, 129279491, 116490423, 238075133, 1483634, "SRX19234273", "SRS16638731", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.1186, 0.92133, 0.11281, 0.53473, 0.99391, 0.89818, 0.6282, 0.56941, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73960, "SRR23291003", "SRX19234273", "SRS16638731", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 1", "GSM7016813", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016813", "GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq", "GSM7016813 r1", "GSM7016813", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-025_HCMYKBGXC_S8_L002_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L002_R2_001.fastq.gz", "fastq fastq", 633345022.0, 7364477.0, "GSM7016813 r2", "0:26 1:60", "A:150874121;C:127629476;G:118171343;T:235389766;N:1280316", 26, 60, null, null, 150874121, 127629476, 118171343, 235389766, 1280316, "SRX19234273", "SRS16638731", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11665, 0.91596, 0.11139, 0.53318, 0.99425, 0.89822, 0.64949, 0.56009, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73961, "SRR23291004", "SRX19234273", "SRS16638731", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 1", "GSM7016813", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016813", "GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq", "GSM7016813 r1", "GSM7016813", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-025_HCMYKBGXC_S8_L003_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L003_R2_001.fastq.gz", "fastq fastq", 643723416.0, 7485156.0, "GSM7016813 r3", "0:26 1:60", "A:154277144;C:130529094;G:117635488;T:240275453;N:1006237", 26, 60, null, null, 154277144, 130529094, 117635488, 240275453, 1006237, "SRX19234273", "SRS16638731", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11809, 0.9216, 0.11258, 0.53566, 0.99397, 0.89871, 0.63435, 0.55308, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73962, "SRR23291005", "SRX19234273", "SRS16638731", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 21dpi 1", "GSM7016813", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing", "zfCM 21dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi", "GSM7016813", "GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq", "GSM7016813 r1", "GSM7016813", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-PN-025_HCMYKBGXC_S8_L004_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L004_R2_001.fastq.gz", "fastq fastq", 632759362.0, 7357667.0, "GSM7016813 r4", "0:26 1:60", "A:150797181;C:127674217;G:117974605;T:235361625;N:951734", 26, 60, null, null, 150797181, 127674217, 117974605, 235361625, 951734, "SRX19234273", "SRS16638731", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11662, 0.91609, 0.11147, 0.53237, 0.99381, 0.89775, 0.65781, 0.55524, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73963, "SRR23291006", "SRX19234272", "SRS16638730", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 3", "GSM7016812", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 3", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016812", "GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq", "GSM7016812 r1", "GSM7016812", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz", "fastq fastq", 929999528.0, 10813948.0, "GSM7016812 r1", "0:26 1:60", "A:240334465;C:174255952;G:184260587;T:330943403;N:205121", 26, 60, null, null, 240334465, 174255952, 184260587, 330943403, 205121, "SRX19234272", "SRS16638730", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11116, 0.87404, 0.10307, 0.43901, 0.99178, 0.93034, 0.6268, 0.44639, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73964, "SRR23291007", "SRX19234272", "SRS16638730", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 3", "GSM7016812", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 3", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016812", "GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq", "GSM7016812 r1", "GSM7016812", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz", "fastq fastq", 987824896.0, 11486336.0, "GSM7016812 r2", "0:26 1:60", "A:251121714;C:184449811;G:201317783;T:350692225;N:243363", 26, 60, null, null, 251121714, 184449811, 201317783, 350692225, 243363, "SRX19234272", "SRS16638730", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11269, 0.87873, 0.10426, 0.44461, 0.99172, 0.92506, 0.6241, 0.4506, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73965, "SRR23291008", "SRX19234272", "SRS16638730", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 3", "GSM7016812", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 3", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016812", "GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq", "GSM7016812 r1", "GSM7016812", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz", "fastq fastq", 959933032.0, 11162012.0, "GSM7016812 r3", "0:26 1:60", "A:247983556;C:179564753;G:190342582;T:341858456;N:183685", 26, 60, null, null, 247983556, 179564753, 190342582, 341858456, 183685, "SRX19234272", "SRS16638730", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11176, 0.87161, 0.10342, 0.43986, 0.99155, 0.93026, 0.63442, 0.44405, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73966, "SRR23291009", "SRX19234272", "SRS16638730", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 3", "GSM7016812", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 3", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016812", "GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq", "GSM7016812 r1", "GSM7016812", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz", "fastq fastq", 798370766.0, 9283381.0, "GSM7016812 r4", "0:26 1:60", "A:205538880;C:148510556;G:161196381;T:282964175;N:160774", 26, 60, null, null, 205538880, 148510556, 161196381, 282964175, 160774, "SRX19234272", "SRS16638730", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11014, 0.87018, 0.10209, 0.43668, 0.9921, 0.93346, 0.56645, 0.44683, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73967, "SRR23291010", "SRX19234271", "SRS16638729", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 2", "GSM7016811", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016811", "GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq", "GSM7016811 r1", "GSM7016811", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz", "fastq fastq", 806178534.0, 9374169.0, "GSM7016811 r1", "0:26 1:60", "A:213590554;C:148614157;G:163804315;T:279996916;N:172592", 26, 60, null, null, 213590554, 148614157, 163804315, 279996916, 172592, "SRX19234271", "SRS16638729", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10778, 0.79221, 0.1011, 0.39378, 0.99299, 0.93695, 0.65894, 0.39542, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73968, "SRR23291011", "SRX19234271", "SRS16638729", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 2", "GSM7016811", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016811", "GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq", "GSM7016811 r1", "GSM7016811", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz", "fastq fastq", 874594286.0, 10169701.0, "GSM7016811 r2", "0:26 1:60", "A:227213153;C:160851586;G:182364146;T:303951184;N:214217", 26, 60, null, null, 227213153, 160851586, 182364146, 303951184, 214217, "SRX19234271", "SRS16638729", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11066, 0.80318, 0.10409, 0.40131, 0.99289, 0.9333, 0.66859, 0.40896, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73969, "SRR23291012", "SRX19234271", "SRS16638729", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 2", "GSM7016811", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016811", "GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq", "GSM7016811 r1", "GSM7016811", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz", "fastq fastq", 831835860.0, 9672510.0, "GSM7016811 r3", "0:26 1:60", "A:220300204;C:153061412;G:168938657;T:289375449;N:160138", 26, 60, null, null, 220300204, 153061412, 168938657, 289375449, 160138, "SRX19234271", "SRS16638729", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10977, 0.78663, 0.1033, 0.39172, 0.99297, 0.93669, 0.64493, 0.36881, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73970, "SRR23291013", "SRX19234271", "SRS16638729", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 2", "GSM7016811", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 2", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016811", "GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq", "GSM7016811 r1", "GSM7016811", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz", "fastq fastq", 692573136.0, 8053176.0, "GSM7016811 r4", "0:26 1:60", "A:182418113;C:126757471;G:143869511;T:239393143;N:134898", 26, 60, null, null, 182418113, 126757471, 143869511, 239393143, 134898, "SRX19234271", "SRS16638729", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10826, 0.81364, 0.10182, 0.40464, 0.9931, 0.94034, 0.66059, 0.40686, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73971, "SRR23291015", "SRX19234270", "SRS16638728", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 1", "GSM7016810", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016810", "GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq", "GSM7016810 r1", "GSM7016810", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz", "fastq fastq", 471703034.0, 5484919.0, "GSM7016810 r1", "0:26 1:60", "A:125045012;C:89627491;G:85413855;T:171466861;N:149815", 26, 60, null, null, 125045012, 89627491, 85413855, 171466861, 149815, "SRX19234270", "SRS16638728", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10906, 0.67997, 0.10214, 0.30398, 0.99117, 0.94209, 0.6357, 0.45559, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73972, "SRR23291016", "SRX19234270", "SRS16638728", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 1", "GSM7016810", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016810", "GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq", "GSM7016810 r1", "GSM7016810", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz", "fastq fastq", 489372938.0, 5690383.0, "GSM7016810 r2", "0:26 1:60", "A:131516821;C:92202683;G:88685608;T:176824985;N:142841", 26, 60, null, null, 131516821, 92202683, 88685608, 176824985, 142841, "SRX19234270", "SRS16638728", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11042, 0.68087, 0.10314, 0.3043, 0.99145, 0.94882, 0.5723, 0.46048, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73973, "SRR23291017", "SRX19234270", "SRS16638728", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 1", "GSM7016810", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016810", "GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq", "GSM7016810 r1", "GSM7016810", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz", "fastq fastq", 407735288.0, 4741108.0, "GSM7016810 r3", "0:26 1:60", "A:108841476;C:77418215;G:73171345;T:148203998;N:100254", 26, 60, null, null, 108841476, 77418215, 73171345, 148203998, 100254, "SRX19234270", "SRS16638728", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10889, 0.67068, 0.10168, 0.29526, 0.99117, 0.9471, 0.66379, 0.42801, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [73974, "SRR23291018", "SRX19234270", "SRS16638728", "SRP420309", "PRJNA929990", "Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration", "GSE224156", "Other", "Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat\u2013containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.", null, "pubmed:37200435", null, "zfCM 7dpi 1", "GSM7016810", null, "source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing", "zfCM 7dpi 1", "Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.", "Heart", "Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi", "GSM7016810", "GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq", "GSM7016810 r1", "GSM7016810", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75\u2005bp read length on the Illumina NextSeq platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP420309", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz", "fastq fastq", 505539304.0, 5878364.0, "GSM7016810 r4", "0:26 1:60", "A:135189083;C:94908231;G:92431583;T:182885125;N:125282", 26, 60, null, null, 135189083, 94908231, 92431583, 182885125, 125282, "SRX19234270", "SRS16638728", "SRA1583767", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10989, 0.68603, 0.10295, 0.30544, 0.99119, 0.94783, 0.65617, 0.41933, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-01-31", "Undetermined", "Undetermined", "Heart", 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