run_metadata: 11019
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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| 11019 | ERR9750935 | ERX9298874 | ERS12023660 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 2 3d post amputation | SAMEA14418102 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 2 3d post amputation p | Expt 2 3d post amputation p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 16111486440.0 | 119344344.0 | E MTAB 10643:Expt 2 3d post amputation | 0:10 1:10 2:28 3:87 | A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227 | 10 | 10 | 28 | 87 | 2610144058 | 2617445332 | 2496763759 | 2656876552 | 1728227 | ERX9298874 | ERS12023660 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.94868 | 0.07071 | 0.89221 | 0.54333 | 87 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System |