{"database": "metadata", "table": "run_metadata", "rows": [[25327, "SRR25868016", "SRX21589422", "SRS18766995", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "SVCV  scRNAseq Kidney leukocyte", "GSM7749528", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing", "SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV", "GSM7749528", "GSM7749528: SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749528 r1", "GSM7749528", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz", "fastq fastq", 48037908933.0, 403679907.0, "GSM7749528 r1", "0:28 1:91", "A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672", 28, 91, null, null, 13476452185, 10712519121, 11200837365, 12646404590, 1695672, "SRX21589422", "SRS18766995", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00795, 0.92383, 0.00261, 0.14, 0.98948, 0.7806, 0.36862, 0.54549, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal 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": ["25327"], "units": {}, "query_ms": 10.263053998642135}