{"database": "metadata", "table": "run_metadata", "rows": [[11021, "ERR9750933", "ERX9298872", "ERS12023658", "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", null, "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 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 1 Uninjured", "SAMEA14418100", "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:SAMEA14418100|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 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle", "E MTAB 10643:Expt 1 Uninjured p", "Expt 1 Uninjured 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 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:n1|Experimental Factor: treatment:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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", "E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 8575585211.0, 67524293.0, "E MTAB 10643:Expt 1 Uninjured", "0:8 1:28 2:91", "A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801", 8, 28, 91, null, 1801503847, 1312196506, 1367890726, 1663053783, 65801, "ERX9298872", "ERS12023658", "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, 0.9169, null, 0.11202, null, 0.81576, null, 0.54253, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2022-05-20", "Adult", "Adult", "Heart", "Cardiovascular System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["11021"], "units": {}, "query_ms": 10.557144996710122}