run_metadata
40 rows where technology = "fluidigm" and tissue_curation_coarse = "Cardiovascular System"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40168 | 40168 | SRR2968466 | SRX1457885 | SRS1185406 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP40 | GSM1959709 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP40 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959709 | GSM1959709: Sample KP40; Danio rerio; RNA Seq | GSM1959709 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959709 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP40_CAGAGAGG-ACTGCATA_R1.fastq.gz KP40_CAGAGAGG-ACTGCATA_R2.fastq.gz | fastq fastq | 1057620252.0 | 10368826.0 | GSM1959709 r1 | 0:51 1:51 | A:283533359;C:244321250;G:245847121;T:283599722;N:318800 | 51 | 51 | 283533359 | 244321250 | 245847121 | 283599722 | 318800 | SRX1457885 | SRS1185406 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76357 | 0.76735 | 0.13867 | 0.14039 | 0.82655 | 0.82964 | 0.48721 | 0.44534 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40169 | 40169 | SRR2968465 | SRX1457884 | SRS1185407 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP39 | GSM1959708 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP39 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959708 | GSM1959708: Sample KP39; Danio rerio; RNA Seq | GSM1959708 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959708 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP39_CAGAGAGG-GTAAGGAG_R1.fastq.gz KP39_CAGAGAGG-GTAAGGAG_R2.fastq.gz | fastq fastq | 836720892.0 | 8203146.0 | GSM1959708 r1 | 0:51 1:51 | A:233855273;C:181887230;G:183940925;T:236839998;N:197466 | 51 | 51 | 233855273 | 181887230 | 183940925 | 236839998 | 197466 | SRX1457884 | SRS1185407 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.74388 | 0.75136 | 0.34441 | 0.34905 | 0.97173 | 0.97246 | 0.57093 | 0.57077 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40170 | 40170 | SRR2968464 | SRX1457883 | SRS1185408 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP38 | GSM1959707 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP38 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959707 | GSM1959707: Sample KP38; Danio rerio; RNA Seq | GSM1959707 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959707 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP38_CAGAGAGG-AGAGTAGA_R1.fastq.gz KP38_CAGAGAGG-AGAGTAGA_R2.fastq.gz | fastq fastq | 835878168.0 | 8194884.0 | GSM1959707 r1 | 0:51 1:51 | A:230311138;C:186569541;G:187836943;T:230971761;N:188785 | 51 | 51 | 230311138 | 186569541 | 187836943 | 230971761 | 188785 | SRX1457883 | SRS1185408 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.80225 | 0.80655 | 0.23659 | 0.24176 | 0.95343 | 0.95503 | 0.44336 | 0.43957 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40171 | 40171 | SRR2968463 | SRX1457882 | SRS1185409 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP37 | GSM1959706 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP37 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959706 | GSM1959706: Sample KP37; Danio rerio; RNA Seq | GSM1959706 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959706 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP37_CAGAGAGG-TATCCTCT_R1.fastq.gz KP37_CAGAGAGG-TATCCTCT_R2.fastq.gz | fastq fastq | 802409316.0 | 7866758.0 | GSM1959706 r1 | 0:51 1:51 | A:219583488;C:179155768;G:180744232;T:222683589;N:242239 | 51 | 51 | 219583488 | 179155768 | 180744232 | 222683589 | 242239 | SRX1457882 | SRS1185409 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.70494 | 0.71211 | 0.22141 | 0.22563 | 0.96895 | 0.96928 | 0.44073 | 0.4369 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40172 | 40172 | SRR2968462 | SRX1457881 | SRS1185410 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP36 | GSM1959705 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP36 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959705 | GSM1959705: Sample KP36; Danio rerio; RNA Seq | GSM1959705 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959705 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP36_CAGAGAGG-CTCTCTAT_R1.fastq.gz KP36_CAGAGAGG-CTCTCTAT_R2.fastq.gz | fastq fastq | 814437360.0 | 7984680.0 | GSM1959705 r1 | 0:51 1:51 | A:224134814;C:180827198;G:181990353;T:227245779;N:239216 | 51 | 51 | 224134814 | 180827198 | 181990353 | 227245779 | 239216 | SRX1457881 | SRS1185410 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.58241 | 0.59172 | 0.29636 | 0.30375 | 0.97991 | 0.98096 | 0.5342 | 0.54149 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40173 | 40173 | SRR2968461 | SRX1457880 | SRS1185411 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP35 | GSM1959704 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP35 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959704 | GSM1959704: Sample KP35; Danio rerio; RNA Seq | GSM1959704 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959704 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP35_CTCTCTAC-ACTGCATA_R1.fastq.gz KP35_CTCTCTAC-ACTGCATA_R2.fastq.gz | fastq fastq | 879876990.0 | 8626245.0 | GSM1959704 r1 | 0:51 1:51 | A:242880860;C:194901817;G:196696322;T:245139130;N:258861 | 51 | 51 | 242880860 | 194901817 | 196696322 | 245139130 | 258861 | SRX1457880 | SRS1185411 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.73158 | 0.737 | 0.31522 | 0.32009 | 0.9671 | 0.96855 | 0.49896 | 0.50832 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40174 | 40174 | SRR2968460 | SRX1457879 | SRS1185412 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP34 | GSM1959703 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP34 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959703 | GSM1959703: Sample KP34; Danio rerio; RNA Seq | GSM1959703 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959703 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP34_CTCTCTAC-GTAAGGAG_R1.fastq.gz KP34_CTCTCTAC-GTAAGGAG_R2.fastq.gz | fastq fastq | 530302590.0 | 5199045.0 | GSM1959703 r1 | 0:51 1:51 | A:125449980;C:137910409;G:138880104;T:127935495;N:126602 | 51 | 51 | 125449980 | 137910409 | 138880104 | 127935495 | 126602 | SRX1457879 | SRS1185412 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.09313 | 0.09794 | 0.01332 | 0.01452 | 0.99243 | 0.9932 | 0.93637 | 0.93172 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40175 | 40175 | SRR2968459 | SRX1457878 | SRS1185413 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP33 | GSM1959702 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP33 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959702 | GSM1959702: Sample KP33; Danio rerio; RNA Seq | GSM1959702 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959702 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP33_CTCTCTAC-AGAGTAGA_R1.fastq.gz KP33_CTCTCTAC-AGAGTAGA_R2.fastq.gz | fastq fastq | 702121590.0 | 6883545.0 | GSM1959702 r1 | 0:51 1:51 | A:177259877;C:172663803;G:174696764;T:177343178;N:157968 | 51 | 51 | 177259877 | 172663803 | 174696764 | 177343178 | 157968 | SRX1457878 | SRS1185413 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.51385 | 0.52475 | 0.02387 | 0.02469 | 0.98662 | 0.988 | 0.33323 | 0.26048 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40176 | 40176 | SRR2968458 | SRX1457877 | SRS1185414 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP32 | GSM1959701 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP32 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959701 | GSM1959701: Sample KP32; Danio rerio; RNA Seq | GSM1959701 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959701 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP32_CTCTCTAC-TATCCTCT_R1.fastq.gz KP32_CTCTCTAC-TATCCTCT_R2.fastq.gz | fastq fastq | 841118214.0 | 8246257.0 | GSM1959701 r1 | 0:51 1:51 | A:226923227;C:192290067;G:193443501;T:228207490;N:253929 | 51 | 51 | 226923227 | 192290067 | 193443501 | 228207490 | 253929 | SRX1457877 | SRS1185414 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.68864 | 0.69538 | 0.16992 | 0.173 | 0.97378 | 0.97445 | 0.43009 | 0.42506 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40177 | 40177 | SRR2968457 | SRX1457876 | SRS1185415 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP31 | GSM1959700 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP31 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959700 | GSM1959700: Sample KP31; Danio rerio; RNA Seq | GSM1959700 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959700 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP31_CTCTCTAC-CTCTCTAT_R1.fastq.gz KP31_CTCTCTAC-CTCTCTAT_R2.fastq.gz | fastq fastq | 897671706.0 | 8800703.0 | GSM1959700 r1 | 0:51 1:51 | A:246982191;C:200919612;G:202035872;T:247462202;N:271829 | 51 | 51 | 246982191 | 200919612 | 202035872 | 247462202 | 271829 | SRX1457876 | SRS1185415 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7947 | 0.7971 | 0.23998 | 0.24233 | 0.9625 | 0.96307 | 0.43428 | 0.44592 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40178 | 40178 | SRR2968456 | SRX1457875 | SRS1185416 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP30 | GSM1959699 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP30 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959699 | GSM1959699: Sample KP30; Danio rerio; RNA Seq | GSM1959699 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959699 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP30_TAGGCATG-ACTGCATA_R1.fastq.gz KP30_TAGGCATG-ACTGCATA_R2.fastq.gz | fastq fastq | 840697464.0 | 8242132.0 | GSM1959699 r1 | 0:51 1:51 | A:229560852;C:189263205;G:190573999;T:231061385;N:238023 | 51 | 51 | 229560852 | 189263205 | 190573999 | 231061385 | 238023 | SRX1457875 | SRS1185416 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7282 | 0.73495 | 0.19781 | 0.20144 | 0.96747 | 0.96846 | 0.4129 | 0.40756 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40179 | 40179 | SRR2968455 | SRX1457874 | SRS1185417 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP29 | GSM1959698 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP29 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959698 | GSM1959698: Sample KP29; Danio rerio; RNA Seq | GSM1959698 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959698 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP29_TAGGCATG-GTAAGGAG_R1.fastq.gz KP29_TAGGCATG-GTAAGGAG_R2.fastq.gz | fastq fastq | 731773602.0 | 7174251.0 | GSM1959698 r1 | 0:51 1:51 | A:206943127;C:156494362;G:158179677;T:209990471;N:165965 | 51 | 51 | 206943127 | 156494362 | 158179677 | 209990471 | 165965 | SRX1457874 | SRS1185417 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.65896 | 0.66545 | 0.44181 | 0.4484 | 0.97344 | 0.97374 | 0.39976 | 0.40584 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40180 | 40180 | SRR2968454 | SRX1457873 | SRS1185418 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP28 | GSM1959697 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP28 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959697 | GSM1959697: Sample KP28; Danio rerio; RNA Seq | GSM1959697 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959697 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP28_TAGGCATG-AGAGTAGA_R1.fastq.gz KP28_TAGGCATG-AGAGTAGA_R2.fastq.gz | fastq fastq | 610756314.0 | 5987807.0 | GSM1959697 r1 | 0:51 1:51 | A:168561813;C:135881390;G:137142260;T:169047160;N:123691 | 51 | 51 | 168561813 | 135881390 | 137142260 | 169047160 | 123691 | SRX1457873 | SRS1185418 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82068 | 0.82379 | 0.2075 | 0.21165 | 0.95619 | 0.95789 | 0.43858 | 0.42372 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40181 | 40181 | SRR2968453 | SRX1457872 | SRS1185419 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP27 | GSM1959696 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP27 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959696 | GSM1959696: Sample KP27; Danio rerio; RNA Seq | GSM1959696 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959696 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP27_TAGGCATG-TATCCTCT_R1.fastq.gz KP27_TAGGCATG-TATCCTCT_R2.fastq.gz | fastq fastq | 781484424.0 | 7661612.0 | GSM1959696 r1 | 0:51 1:51 | A:212034731;C:176627403;G:178333528;T:214264629;N:224133 | 51 | 51 | 212034731 | 176627403 | 178333528 | 214264629 | 224133 | SRX1457872 | SRS1185419 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.61712 | 0.62713 | 0.23077 | 0.23648 | 0.9792 | 0.97944 | 0.39126 | 0.38932 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40182 | 40182 | SRR2968452 | SRX1457871 | SRS1185420 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP26 | GSM1959695 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP26 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959695 | GSM1959695: Sample KP26; Danio rerio; RNA Seq | GSM1959695 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959695 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP26_TAGGCATG-CTCTCTAT_R1.fastq.gz KP26_TAGGCATG-CTCTCTAT_R2.fastq.gz | fastq fastq | 780739926.0 | 7654313.0 | GSM1959695 r1 | 0:51 1:51 | A:218146933;C:170676228;G:171957248;T:219735082;N:224435 | 51 | 51 | 218146933 | 170676228 | 171957248 | 219735082 | 224435 | SRX1457871 | SRS1185420 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.78797 | 0.79538 | 0.35334 | 0.36142 | 0.96274 | 0.96349 | 0.47377 | 0.4735 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40183 | 40183 | SRR2968451 | SRX1457870 | SRS1185421 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP25 | GSM1959694 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP25 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959694 | GSM1959694: Sample KP25; Danio rerio; RNA Seq | GSM1959694 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959694 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP25_GGACTCCT-ACTGCATA_R1.fastq.gz KP25_GGACTCCT-ACTGCATA_R2.fastq.gz | fastq fastq | 859091634.0 | 8422467.0 | GSM1959694 r1 | 0:51 1:51 | A:236569798;C:191447789;G:192382830;T:238434022;N:257195 | 51 | 51 | 236569798 | 191447789 | 192382830 | 238434022 | 257195 | SRX1457870 | SRS1185421 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.759 | 0.76468 | 0.27302 | 0.27761 | 0.95554 | 0.95649 | 0.46406 | 0.47077 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40184 | 40184 | SRR2968450 | SRX1457869 | SRS1185422 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP24 | GSM1959693 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP24 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959693 | GSM1959693: Sample KP24; Danio rerio; RNA Seq | GSM1959693 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959693 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP24_GGACTCCT-GTAAGGAG_R1.fastq.gz KP24_GGACTCCT-GTAAGGAG_R2.fastq.gz | fastq fastq | 459382704.0 | 4503752.0 | GSM1959693 r1 | 0:51 1:51 | A:114887340;C:111878133;G:113634471;T:118873760;N:109000 | 51 | 51 | 114887340 | 111878133 | 113634471 | 118873760 | 109000 | SRX1457869 | SRS1185422 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.29195 | 0.30626 | 0.06586 | 0.07052 | 0.98397 | 0.98384 | 0.7621 | 0.75529 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40185 | 40185 | SRR2968449 | SRX1457868 | SRS1185423 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP23 | GSM1959692 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP23 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959692 | GSM1959692: Sample KP23; Danio rerio; RNA Seq | GSM1959692 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959692 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP23_GGACTCCT-AGAGTAGA_R1.fastq.gz KP23_GGACTCCT-AGAGTAGA_R2.fastq.gz | fastq fastq | 659521494.0 | 6465897.0 | GSM1959692 r1 | 0:51 1:51 | A:178790202;C:149883938;G:150983815;T:179718576;N:144963 | 51 | 51 | 178790202 | 149883938 | 150983815 | 179718576 | 144963 | SRX1457868 | SRS1185423 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76779 | 0.77368 | 0.18286 | 0.18729 | 0.96948 | 0.96988 | 0.46781 | 0.47575 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40186 | 40186 | SRR2968448 | SRX1457867 | SRS1185424 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP22 | GSM1959691 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP22 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959691 | GSM1959691: Sample KP22; Danio rerio; RNA Seq | GSM1959691 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959691 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP22_GGACTCCT-TATCCTCT_R1.fastq.gz KP22_GGACTCCT-TATCCTCT_R2.fastq.gz | fastq fastq | 665437800.0 | 6523900.0 | GSM1959691 r1 | 0:51 1:51 | A:186143553;C:145046910;G:145792876;T:188254173;N:200288 | 51 | 51 | 186143553 | 145046910 | 145792876 | 188254173 | 200288 | SRX1457867 | SRS1185424 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.78988 | 0.7988 | 0.23272 | 0.23796 | 0.9613 | 0.9623 | 0.40863 | 0.41821 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40187 | 40187 | SRR2968447 | SRX1457866 | SRS1185425 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP21 | GSM1959690 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP21 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959690 | GSM1959690: Sample KP21; Danio rerio; RNA Seq | GSM1959690 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959690 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP21_GGACTCCT-CTCTCTAT_R1.fastq.gz KP21_GGACTCCT-CTCTCTAT_R2.fastq.gz | fastq fastq | 765085884.0 | 7500842.0 | GSM1959690 r1 | 0:51 1:51 | A:209306735;C:171106728;G:172589951;T:211844805;N:237665 | 51 | 51 | 209306735 | 171106728 | 172589951 | 211844805 | 237665 | SRX1457866 | SRS1185425 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.72371 | 0.73294 | 0.27277 | 0.27804 | 0.97143 | 0.97256 | 0.55072 | 0.54783 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40188 | 40188 | SRR2968446 | SRX1457865 | SRS1185426 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP20 | GSM1959689 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP20 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959689 | GSM1959689: Sample KP20; Danio rerio; RNA Seq | GSM1959689 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959689 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP20_TCCTGAGC-ACTGCATA_R1.fastq.gz KP20_TCCTGAGC-ACTGCATA_R2.fastq.gz | fastq fastq | 543216198.0 | 5325649.0 | GSM1959689 r1 | 0:51 1:51 | A:130111136;C:139338862;G:140806793;T:132795809;N:163598 | 51 | 51 | 130111136 | 139338862 | 140806793 | 132795809 | 163598 | SRX1457865 | SRS1185426 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.15752 | 0.16626 | 0.01611 | 0.01706 | 0.99062 | 0.99226 | 0.90887 | 0.90965 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40189 | 40189 | SRR2968445 | SRX1457864 | SRS1185427 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP19 | GSM1959688 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP19 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959688 | GSM1959688: Sample KP19; Danio rerio; RNA Seq | GSM1959688 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959688 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP19_TCCTGAGC-GTAAGGAG_R1.fastq.gz KP19_TCCTGAGC-GTAAGGAG_R2.fastq.gz | fastq fastq | 679334484.0 | 6660142.0 | GSM1959688 r1 | 0:51 1:51 | A:187051480;C:151121998;G:152297545;T:188715899;N:147562 | 51 | 51 | 187051480 | 151121998 | 152297545 | 188715899 | 147562 | SRX1457864 | SRS1185427 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7866 | 0.79407 | 0.22875 | 0.23386 | 0.96575 | 0.96552 | 0.43227 | 0.45264 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40190 | 40190 | SRR2968444 | SRX1457863 | SRS1185428 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP18 | GSM1959687 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP18 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959687 | GSM1959687: Sample KP18; Danio rerio; RNA Seq | GSM1959687 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959687 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP18_TCCTGAGC-AGAGTAGA_R1.fastq.gz KP18_TCCTGAGC-AGAGTAGA_R2.fastq.gz | fastq fastq | 641049906.0 | 6284803.0 | GSM1959687 r1 | 0:51 1:51 | A:175031019;C:144143474;G:145394298;T:176339875;N:141240 | 51 | 51 | 175031019 | 144143474 | 145394298 | 176339875 | 141240 | SRX1457863 | SRS1185428 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7934 | 0.79898 | 0.24196 | 0.2479 | 0.95893 | 0.9598 | 0.39391 | 0.39181 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40191 | 40191 | SRR2968443 | SRX1457862 | SRS1185429 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP17 | GSM1959686 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP17 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959686 | GSM1959686: Sample KP17; Danio rerio; RNA Seq | GSM1959686 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959686 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP17_TCCTGAGC-TATCCTCT_R1.fastq.gz KP17_TCCTGAGC-TATCCTCT_R2.fastq.gz | fastq fastq | 446775504.0 | 4380152.0 | GSM1959686 r1 | 0:51 1:51 | A:111578533;C:109198448;G:110776525;T:115086866;N:135132 | 51 | 51 | 111578533 | 109198448 | 110776525 | 115086866 | 135132 | SRX1457862 | SRS1185429 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.28419 | 0.29939 | 0.06797 | 0.07225 | 0.98289 | 0.98378 | 0.778 | 0.75243 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40192 | 40192 | SRR2968442 | SRX1457861 | SRS1185430 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP16 | GSM1959685 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP16 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959685 | GSM1959685: Sample KP16; Danio rerio; RNA Seq | GSM1959685 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959685 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP16_TCCTGAGC-CTCTCTAT_R1.fastq.gz KP16_TCCTGAGC-CTCTCTAT_R2.fastq.gz | fastq fastq | 692282466.0 | 6787083.0 | GSM1959685 r1 | 0:51 1:51 | A:189795491;C:154553440;G:155323657;T:192401712;N:208166 | 51 | 51 | 189795491 | 154553440 | 155323657 | 192401712 | 208166 | SRX1457861 | SRS1185430 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.79142 | 0.79731 | 0.16527 | 0.16819 | 0.95759 | 0.9572 | 0.4286 | 0.43086 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40193 | 40193 | SRR2968441 | SRX1457860 | SRS1185431 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP15 | GSM1959684 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP15 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959684 | GSM1959684: Sample KP15; Danio rerio; RNA Seq | GSM1959684 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959684 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP15_AGGCAGAA-ACTGCATA_R1.fastq.gz KP15_AGGCAGAA-ACTGCATA_R2.fastq.gz | fastq fastq | 809730570.0 | 7938535.0 | GSM1959684 r1 | 0:51 1:51 | A:222748248;C:181137297;G:181895010;T:223711434;N:238581 | 51 | 51 | 222748248 | 181137297 | 181895010 | 223711434 | 238581 | SRX1457860 | SRS1185431 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82855 | 0.83316 | 0.19743 | 0.20117 | 0.933 | 0.93413 | 0.48016 | 0.48161 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40194 | 40194 | SRR2968440 | SRX1457859 | SRS1185432 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP14 | GSM1959683 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP14 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959683 | GSM1959683: Sample KP14; Danio rerio; RNA Seq | GSM1959683 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959683 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP14_AGGCAGAA-GTAAGGAG_R1.fastq.gz KP14_AGGCAGAA-GTAAGGAG_R2.fastq.gz | fastq fastq | 719230968.0 | 7051284.0 | GSM1959683 r1 | 0:51 1:51 | A:194927824;C:163566192;G:164765634;T:195815160;N:156158 | 51 | 51 | 194927824 | 163566192 | 164765634 | 195815160 | 156158 | SRX1457859 | SRS1185432 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.70333 | 0.71022 | 0.20537 | 0.20983 | 0.97437 | 0.97423 | 0.49029 | 0.49675 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40195 | 40195 | SRR2968439 | SRX1457858 | SRS1185433 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP13 | GSM1959682 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP13 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959682 | GSM1959682: Sample KP13; Danio rerio; RNA Seq | GSM1959682 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959682 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP13_AGGCAGAA-AGAGTAGA_R1.fastq.gz KP13_AGGCAGAA-AGAGTAGA_R2.fastq.gz | fastq fastq | 670420602.0 | 6572751.0 | GSM1959682 r1 | 0:51 1:51 | A:183200862;C:151496578;G:152546937;T:183041619;N:134606 | 51 | 51 | 183200862 | 151496578 | 152546937 | 183041619 | 134606 | SRX1457858 | SRS1185433 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76244 | 0.76756 | 0.21376 | 0.21794 | 0.96544 | 0.96581 | 0.49113 | 0.50419 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40196 | 40196 | SRR2968438 | SRX1457857 | SRS1185434 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP12 | GSM1959681 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP12 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959681 | GSM1959681: Sample KP12; Danio rerio; RNA Seq | GSM1959681 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959681 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP12_AGGCAGAA-TATCCTCT_R1.fastq.gz KP12_AGGCAGAA-TATCCTCT_R2.fastq.gz | fastq fastq | 733517394.0 | 7191347.0 | GSM1959681 r1 | 0:51 1:51 | A:203973287;C:161740792;G:162503121;T:205085052;N:215142 | 51 | 51 | 203973287 | 161740792 | 162503121 | 205085052 | 215142 | SRX1457857 | SRS1185434 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.73987 | 0.74727 | 0.26293 | 0.26931 | 0.96692 | 0.96828 | 0.47118 | 0.48277 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40197 | 40197 | SRR2968437 | SRX1457856 | SRS1185435 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP11 | GSM1959680 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP11 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959680 | GSM1959680: Sample KP11; Danio rerio; RNA Seq | GSM1959680 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959680 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP11_AGGCAGAA-CTCTCTAT_R1.fastq.gz KP11_AGGCAGAA-CTCTCTAT_R2.fastq.gz | fastq fastq | 694641930.0 | 6810215.0 | GSM1959680 r1 | 0:51 1:51 | A:186479810;C:159537888;G:161650457;T:186768027;N:205748 | 51 | 51 | 186479810 | 159537888 | 161650457 | 186768027 | 205748 | SRX1457856 | SRS1185435 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.77343 | 0.7785 | 0.21899 | 0.22166 | 0.96591 | 0.96609 | 0.46452 | 0.49761 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40198 | 40198 | SRR2968436 | SRX1457855 | SRS1185436 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP10 | GSM1959679 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP10 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959679 | GSM1959679: Sample KP10; Danio rerio; RNA Seq | GSM1959679 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959679 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP10_CGTACTAG-ACTGCATA_R1.fastq.gz KP10_CGTACTAG-ACTGCATA_R2.fastq.gz | fastq fastq | 685215906.0 | 6717803.0 | GSM1959679 r1 | 0:51 1:51 | A:182783777;C:159470626;G:160436500;T:182320016;N:204987 | 51 | 51 | 182783777 | 159470626 | 160436500 | 182320016 | 204987 | SRX1457855 | SRS1185436 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82772 | 0.83105 | 0.2043 | 0.20688 | 0.95373 | 0.95465 | 0.45406 | 0.44707 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40199 | 40199 | SRR2968435 | SRX1457854 | SRS1185437 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP9 | GSM1959678 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP9 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959678 | GSM1959678: Sample KP9; Danio rerio; RNA Seq | GSM1959678 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959678 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP9_CGTACTAG-GTAAGGAG_R1.fastq.gz KP9_CGTACTAG-GTAAGGAG_R2.fastq.gz | fastq fastq | 551932098.0 | 5411099.0 | GSM1959678 r1 | 0:51 1:51 | A:153342642;C:121303381;G:122377461;T:154778838;N:129776 | 51 | 51 | 153342642 | 121303381 | 122377461 | 154778838 | 129776 | SRX1457854 | SRS1185437 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.79709 | 0.80596 | 0.27077 | 0.27672 | 0.95 | 0.95142 | 0.47936 | 0.477 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40200 | 40200 | SRR2968434 | SRX1457853 | SRS1185398 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP8 | GSM1959677 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP8 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959677 | GSM1959677: Sample KP8; Danio rerio; RNA Seq | GSM1959677 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959677 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP8_CGTACTAG-AGAGTAGA_R1.fastq.gz KP8_CGTACTAG-AGAGTAGA_R2.fastq.gz | fastq fastq | 714534480.0 | 7005240.0 | GSM1959677 r1 | 0:51 1:51 | A:191434342;C:165417603;G:166779779;T:190738042;N:164714 | 51 | 51 | 191434342 | 165417603 | 166779779 | 190738042 | 164714 | SRX1457853 | SRS1185398 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.69731 | 0.70407 | 0.26985 | 0.27604 | 0.97417 | 0.97561 | 0.45016 | 0.44563 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40201 | 40201 | SRR2968433 | SRX1457852 | SRS1185399 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP7 | GSM1959676 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP7 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959676 | GSM1959676: Sample KP7; Danio rerio; RNA Seq | GSM1959676 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959676 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP7_CGTACTAG-TATCCTCT_R1.fastq.gz KP7_CGTACTAG-TATCCTCT_R2.fastq.gz | fastq fastq | 540102648.0 | 5295124.0 | GSM1959676 r1 | 0:51 1:51 | A:136000723;C:131024642;G:132847890;T:140063894;N:165499 | 51 | 51 | 136000723 | 131024642 | 132847890 | 140063894 | 165499 | SRX1457852 | SRS1185399 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.29483 | 0.30833 | 0.11533 | 0.12459 | 0.98307 | 0.9834 | 0.30473 | 0.30304 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40202 | 40202 | SRR2968432 | SRX1457851 | SRS1185402 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP6 | GSM1959675 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP6 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959675 | GSM1959675: Sample KP6; Danio rerio; RNA Seq | GSM1959675 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959675 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP6_CGTACTAG-CTCTCTAT_R1.fastq.gz KP6_CGTACTAG-CTCTCTAT_R2.fastq.gz | fastq fastq | 727623120.0 | 7133560.0 | GSM1959675 r1 | 0:51 1:51 | A:187458228;C:175169703;G:176202805;T:188567551;N:224833 | 51 | 51 | 187458228 | 175169703 | 176202805 | 188567551 | 224833 | SRX1457851 | SRS1185402 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.60168 | 0.60687 | 0.2039 | 0.20684 | 0.97589 | 0.97652 | 0.48458 | 0.48815 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40203 | 40203 | SRR2968431 | SRX1457850 | SRS1185400 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP5 | GSM1959674 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP5 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959674 | GSM1959674: Sample KP5; Danio rerio; RNA Seq | GSM1959674 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959674 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP5_TAAGGCGA-ACTGCATA_R1.fastq.gz KP5_TAAGGCGA-ACTGCATA_R2.fastq.gz | fastq fastq | 554516064.0 | 5436432.0 | GSM1959674 r1 | 0:51 1:51 | A:135355365;C:141324408;G:141559086;T:136117221;N:159984 | 51 | 51 | 135355365 | 141324408 | 141559086 | 136117221 | 159984 | SRX1457850 | SRS1185400 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.81675 | 0.8183 | 0.07186 | 0.07288 | 0.93695 | 0.93819 | 0.46802 | 0.47319 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40204 | 40204 | SRR2968430 | SRX1457849 | SRS1185401 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP4 | GSM1959673 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP4 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959673 | GSM1959673: Sample KP4; Danio rerio; RNA Seq | GSM1959673 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959673 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP4_TAAGGCGA-GTAAGGAG_R1.fastq.gz KP4_TAAGGCGA-GTAAGGAG_R2.fastq.gz | fastq fastq | 571891560.0 | 5606780.0 | GSM1959673 r1 | 0:51 1:51 | A:137779848;C:147767737;G:148621338;T:137588687;N:133950 | 51 | 51 | 137779848 | 147767737 | 148621338 | 137588687 | 133950 | SRX1457849 | SRS1185401 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.37677 | 0.384 | 0.09331 | 0.09568 | 0.9893 | 0.98936 | 0.52065 | 0.51305 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40205 | 40205 | SRR2968429 | SRX1457848 | SRS1185403 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP3 | GSM1959672 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP3 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959672 | GSM1959672: Sample KP3; Danio rerio; RNA Seq | GSM1959672 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959672 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP3_TAAGGCGA-AGAGTAGA_R1.fastq.gz KP3_TAAGGCGA-AGAGTAGA_R2.fastq.gz | fastq fastq | 452221590.0 | 4433545.0 | GSM1959672 r1 | 0:51 1:51 | A:114292214;C:111543381;G:112430113;T:113859372;N:96510 | 51 | 51 | 114292214 | 111543381 | 112430113 | 113859372 | 96510 | SRX1457848 | SRS1185403 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76206 | 0.7667 | 0.1482 | 0.15259 | 0.96361 | 0.96477 | 0.42861 | 0.43397 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40206 | 40206 | SRR2968428 | SRX1457847 | SRS1185404 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP2 | GSM1959671 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP2 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959671 | GSM1959671: Sample KP2; Danio rerio; RNA Seq | GSM1959671 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959671 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP2_TAAGGCGA-TATCCTCT_R1.fastq.gz KP2_TAAGGCGA-TATCCTCT_R2.fastq.gz | fastq fastq | 497804574.0 | 4880437.0 | GSM1959671 r1 | 0:51 1:51 | A:127739086;C:120409728;G:121277399;T:128233124;N:145237 | 51 | 51 | 127739086 | 120409728 | 121277399 | 128233124 | 145237 | SRX1457847 | SRS1185404 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.72721 | 0.73133 | 0.19448 | 0.19789 | 0.96394 | 0.96441 | 0.42509 | 0.42064 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40207 | 40207 | SRR2968427 | SRX1457846 | SRS1185405 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP1 | GSM1959670 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP1 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959670 | GSM1959670: Sample KP1; Danio rerio; RNA Seq | GSM1959670 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959670 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP1_TAAGGCGA-CTCTCTAT_R1.fastq.gz KP1_TAAGGCGA-CTCTCTAT_R2.fastq.gz | fastq fastq | 369456138.0 | 3622119.0 | GSM1959670 r1 | 0:51 1:51 | A:92118547;C:94231849;G:93842019;T:89151962;N:111761 | 51 | 51 | 92118547 | 94231849 | 93842019 | 89151962 | 111761 | SRX1457846 | SRS1185405 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.32263 | 0.33307 | 0.00387 | 0.00402 | 0.99423 | 0.99521 | 0.98002 | 0.98282 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;