{"database": "metadata", "table": "run_metadata", "rows": [[31686, "SRR28490931", "SRX24093145", "SRS20882441", "SRP498465", "PRJNA1093008", "Distinct features of the regenerating heart uncovered through comparative single cell profiling", "GSE262689", "Other", "Adult humans respond to heart injury by forming a permanent scar  yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians  the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features  we compared cardiac injury responses in zebrafish and medaka  two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach  we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury  we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes  and an absence of the injury induced interferon response seen in zebrafish. In addition  we found a lack of pro regenerative signals  including nrg1 and retinoic acid  from medaka endothelial and epicardial cells. Finally  we identified alterations in the myocardial structure in medaka  where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka  demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury  3 days  and 14 xxx post injury", null, null, null, "zebrafish uninjured rep1", "GSM8173831", null, "source name:Heart Ventricle|tissue:Heart Ventricle|treatment:Uninjured|geo loc name:missing|collection date:missing", "zebrafish uninjured rep1", "Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings  using GRCz11 v4.3.2 reference Lawson et al.  2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11  ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files", "Heart Ventricle", "Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously Gonz\u00e1lez Rosa et al.  2011. Briefly  0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka  respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonz\u00e1lez Rosa and Mercader  2012. post submersion in liquid nitrogen for at least 2 minutes  the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury  fish were placed back into freshwater tanks to recover  then transferred back into the fish facility for monitoring.", "To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open \u2022 Accepted manuscript in 200 \u00b5l dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37\u00b0C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 \u00b5M strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4\u00b0C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer\u2019s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller", "Wild type T\u00fcbingen zebrafish and CAB medaka  aged 6 month 18 month unless otherwise stated  were used for all experiments. All zebrafish and medaka work was performed at University of Utah\u2019s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah\u2019s animal care and use program.", "tissue:Heart Ventricle|treatment:Uninjured", "GSM8173831", "GSM8173831: zebrafish uninjured rep1; Danio rerio; RNA Seq", "GSM8173831 r1", "GSM8173831", "1", "To prepare cells for scRNA seq  adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts  the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open \u2022 Accepted manuscript in 200 \u00b5l dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37\u00b0C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion  the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 \u00b5M strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4\u00b0C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498465", null, "loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 I1 001.fastq.gz   read2PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 R1 001.fastq.gz   read3PairFiles=18041X1 200623 A00421 0208 BHT77VDMXX S2 L001 R2 001.fastq.gz", "18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_I1_001.fastq.gz 18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_R1_001.fastq.gz 18041X1_200623_A00421_0208_BHT77VDMXX_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 48849838812.0, 262633542.0, "GSM8173831 r1", "0:8 1:28 2:150", "A:13780412427;C:10982740007;G:9382145879;T:12602525920;N:946243", 8, 28, 150, null, 13780412427, 10982740007, 9382145879, 12602525920, 946243, "SRX24093145", "SRS20882441", "SRA1835934", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-03-28", "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": ["31686"], "units": {}, "query_ms": 11.935463000554591}