run_metadata: 15021
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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| 15021 | ERR12352457 | ERX11729319 | ERS17282124 | ERP155844 | PRJEB70944 | The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch | E-MTAB-13603 | Transcriptome Analysis | Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. | ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 | Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR | Trpc6a KO sham 1 | SAMEA114857165 | Institut de Génomique Fonctionnelle | ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857165|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB | The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch | E MTAB 13603:Trpc6a KO sham 1 p | Trpc6a KO sham 1 p | The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch | Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP155844 | Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch | ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20 | 1-Trpc6-KO-sham_R1_001.fastq.gz 1-Trpc6-KO-sham_R2_001.fastq.gz | fastq fastq | 16463891400.0 | 54879638.0 | E MTAB 13603:1 Trpc6 KO sham R | 0:150 1:150 | A:4481016793;C:3727761629;G:3905685351;T:4349193797;N:233830 | 150 | 150 | 4481016793 | 3727761629 | 3905685351 | 4349193797 | 233830 | ERX11729319 | ERS17282124 | ERA27710226 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.95234 | 0.95051 | 0.05908 | 0.05789 | 0.77477 | 0.77605 | 0.49876 | 0.50128 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | 3prime | poly_a | nebnext | bulk | unknown | unknown | United Kingdom | 2023-12-20 | Adult | Adult | Heart | Cardiovascular System |