{"database": "metadata", "table": "run_metadata", "rows": [[74553, "SRR23824393", "SRX19646173", "SRS17013982", "SRP426909", "PRJNA943553", "Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]", "GSE227190", "Transcriptome Analysis", "Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.", "parent bioproject:PRJNA943547", "pubmed:39627536", null, "liver 1 dpi replicate 1", "GSM7092938", null, "source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury", "liver 1 dpi replicate 1", "Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.", "Liver", "Heart cryoinjury or untreated", "Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury", "GSM7092938", "GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq", "GSM7092938 r1", "GSM7092938", "1", "Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-Liver-1_S11_L002_R1_001.fastq.gz 1dpi-Liver-1_S11_L002_R2_001.fastq.gz", "fastq fastq", 4194311652.0, 35545014.0, "GSM7092938 r2", "0:28 1:90", "A:1164793350;C:977205946;G:1001366769;T:1050855725;N:89862", 28, 90, null, null, 1164793350, 977205946, 1001366769, 1050855725, 89862, "SRX19646173", "SRS17013982", "SRA1603354", "Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine", "Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine", 2, 0.0076, 0.9407, 0.0018, 0.08601, 0.99389, 0.86831, 0.256, 0.50037, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-03-12", "Undetermined", "Undetermined", "Liver", "Liver and Biliary 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": ["74553"], "units": {}, "query_ms": 11.750431996915722}