run_metadata: 40188
This data as json
| 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 |
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| 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 |