{"database": "metadata", "table": "run_metadata", "rows": [[61459, "SRR12774373", "SRX9244908", "SRS7477601", "SRP286401", "PRJNA667451", "Cellular drivers of injury response and regeneration in the adult zebrafish heart", "GSE159032", "Transcriptome Analysis", "We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information  we systematically identified potential cellular regulators of cardiomyocyte regeneration  including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium  like the epicardium  gives rise to several distinct fibroblast cell types  and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.", null, "pubmed:35864193", null, "Injured heart Hr12", "GSM4817944", null, "source name:Heart tissue|tissue:heart|condition:Injured|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "Injured heart Hr12", "Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering  Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018  Nature Biotechnology  Briefly  scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps  we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step  we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing  we selected only the most prevalent scar for each combination of barcode and UMI  only the most prevalent UMI for each barcode and scar  and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell  only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally  we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format  Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence  cell barcode  library  cell name  number of reads  CIGAR  UMI sequence  number of libraries where the scar is present in at least two cells  creation probability  number of embryo libraries from LINNAEUS in which this scar is observed  and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building  only the columns \u201cCell\u201d  \u201cp\u201d and \u201cScar\u201d are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org", "Heart tissue", "Cryoinjury: First  fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ  pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart  a small incision was made through the body wall and the pericardium  using microdissection forceps and scissors. Once the pericardial sac was opened  the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper  not allowing fish skin to dry. Then  a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25\u03bcl of 10\u03bcM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi  2dpi for the 3dpi analysis and for later time points  once every two days from 2dpi until the day of sacrifice.", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium  ventricle and bulbus arteriosus  except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards  the tissue was opened carefully with forceps  and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich  0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific  0.1%  while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated  the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA  then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope  and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "Zebrafish were bred  raised  and maintained in accordance with the guidelines of the Max Delbr\u00fcck Center for Molecular Medicine and the local authority for animal protection Landesamt f\u00fcr Gesundheit und Soziales  Berlin  Germany for the use of laboratory animals  and followed the \u2018Principles of Laboratory Animal Care\u2019 NIH publication no. 86 23  revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains\u00a0AB were used for cryoinjury procedure and behavioral analysis.", "tissue:heart|condition:Injured|xxx post injury dpi:3|treatment:non treated|strain:Zebrabow M|10x chemistry version:v2", "GSM4817944", "GSM4817944: Injured heart Hr12; Danio rerio; RNA Seq", "GSM4817944", null, "1", "The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium  ventricle and bulbus arteriosus  except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards  the tissue was opened carefully with forceps  and the heart tissue was incubated at 37 \u00b0C for 30 min in 500\u00b5l HBSS containing Liberase enzyme mix Sigma Aldrich  0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific  0.1%  while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated  the reaction was stopped by adding 500\u00b5l cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4\u00b0C and washed two times with 500\u00b5l cold HBSS containing 0.05% BSA  then filtered through a cell strainer of 35\u00b5m diameter. The quality of the single cell suspension was then confirmed under the microscope  and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics", "GEO Accession:GSM4817944", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP286401", null, null, "Hr12_3dpi_R1.fastq.gz Hr12_3dpi_R2.fastq.gz", "fastq fastq", 28022423836.0, 225987289.0, "GSM4817944 r1", "0:26 1:98", "A:7791062679;C:6561427796;G:6229322338;T:7427193021;N:13418002", 26, 98, null, null, 7791062679, 6561427796, 6229322338, 7427193021, 13418002, "SRX9244908", "SRS7477601", "SRA1138631", "GEO", "Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin", 2, 0.00322, 0.94469, 0.00082, 0.07604, 0.99433, 0.85865, 0.56929, 0.67126, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-10-05", "Undetermined", "Embryo", "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": ["61459"], "units": {}, "query_ms": 6.09117400017567}