run_metadata: 11021

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
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		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									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		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		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		0.11202		0.81576		0.54253		91		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