{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation = \"Spleen\"", "rows": [[71018, "SRR21091734", "SRX17106223", "SRS14681693", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted  knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study  we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "vaccinated+SVCV  scRNAseq", "GSM6469457", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "vaccinated+SVCV  scRNAseq", "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", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469457", "GSM6469457: vaccinated+SVCV  scRNAseq; Danio rerio; RNA Seq", "GSM6469457 r1", "GSM6469457", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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, "SRP392539", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 54148439576.0, 455028904.0, "GSM6469457 r1", "0:28 1:91", "A:15899568894;C:11520113647;G:12620718617;T:14107197313;N:841105", 28, 91, null, null, 15899568894, 11520113647, 12620718617, 14107197313, 841105, "SRX17106223", "SRS14681693", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.01082, 0.82759, 0.00393, 0.19284, 0.99093, 0.82164, 0.42631, 0.61086, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"], [71019, "SRR21091735", "SRX17106222", "SRS14681692", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted  knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study  we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "SVCV  scRNAseq", "GSM6469456", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "SVCV  scRNAseq", "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", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469456", "GSM6469456: SVCV  scRNAseq; Danio rerio; RNA Seq", "GSM6469456 r1", "GSM6469456", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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, "SRP392539", null, null, "SVCV_S1_L001_R1_001.fastq.gz SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 52273900644.0, 439276476.0, "GSM6469456 r1", "0:28 1:91", "A:15161666574;C:11232538299;G:11962650688;T:13914991728;N:2053355", 28, 91, null, null, 15161666574, 11232538299, 11962650688, 13914991728, 2053355, "SRX17106222", "SRS14681692", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.0088, 0.86697, 0.00319, 0.19264, 0.99251, 0.78289, 0.46167, 0.59016, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"], [71020, "SRR21091736", "SRX17106221", "SRS14681691", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted  knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study  we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "PBS  scRNAseq", "GSM6469455", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "PBS  scRNAseq", "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", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469455", "GSM6469455: PBS  scRNAseq; Danio rerio; RNA Seq", "GSM6469455 r1", "GSM6469455", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a  62] Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen 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, "SRP392539", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 48934762310.0, 411216490.0, "GSM6469455 r1", "0:28 1:91", "A:14053810123;C:10679154471;G:11495668034;T:12705747178;N:382504", 28, 91, null, null, 14053810123, 10679154471, 11495668034, 12705747178, 382504, "SRX17106221", "SRS14681691", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00845, 0.84491, 0.00304, 0.17543, 0.99212, 0.78833, 0.45994, 0.6033, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 3, "expanded_columns": [], "expandable_columns": [], "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", 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