{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"10x\" and tissue_curation_coarse = \"Respiratory System\"", "rows": [[68950, "SRR18254619", "SRX14395875", "SRS12205981", "SRP362863", "PRJNA813520", "Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia", "GSE198044", "Transcriptome Analysis", "The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors  neuroepithelial cells NECs. Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   combined normoxia and hypoxia", "GSM5936455", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined", "Gill tissue   combined normoxia and hypoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. 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Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   combined normoxia and hypoxia", "GSM5936455", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined", "Gill tissue   combined normoxia and hypoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. 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Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   14d hypoxia", "GSM5936454", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of hypoxia", "Gill tissue   14d hypoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "genotype:ETvmat2:GFP|treatment:14 days of hypoxia", "GSM5936454", "GSM5936454: Gill tissue   14d hypoxia; Danio rerio; RNA Seq", "GSM5936454 r1", "GSM5936454", "1", "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. 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Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   14d hypoxia", "GSM5936454", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of hypoxia", "Gill tissue   14d hypoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "genotype:ETvmat2:GFP|treatment:14 days of hypoxia", "GSM5936454", "GSM5936454: Gill tissue   14d hypoxia; Danio rerio; RNA Seq", "GSM5936454 r1", "GSM5936454", "1", "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP362863", null, "loader:fastq load.py", "N1_Barcode_I1.fastq.gz N1_Barcode_R1.fastq.gz N1_Barcode_R2.fastq.gz", "fastq fastq fastq", 1417514644.0, 15577084.0, "GSM5936454 r2", "0:8 1:28 2:55", "A:647753176;C:53490237;G:81081706;T:73804327;N:610174", 8, 28, 55, null, 647753176, 53490237, 81081706, 73804327, 610174, "SRX14395874", "SRS12205982", "SRA1392368", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", 1, 0.56618, null, 0.54862, null, 0.99973, null, 0.06569, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2022-03-07", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [68954, "SRR18254623", "SRX14395873", "SRS12205980", "SRP362863", "PRJNA813520", "Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia", "GSE198044", "Transcriptome Analysis", "The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors  neuroepithelial cells NECs. Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   14d normoxia", "GSM5936453", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of normoxia", "Gill tissue   14d normoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "genotype:ETvmat2:GFP|treatment:14 days of normoxia", "GSM5936453", "GSM5936453: Gill tissue   14d normoxia; Danio rerio; RNA Seq", "GSM5936453 r1", "GSM5936453", "1", "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP362863", null, "loader:fastq load.py", "H1_SC_I1.fastq.gz H1_SC_R1.fastq.gz H1_SC_R2.fastq.gz", "fastq fastq fastq", 23487401392.0, 258103312.0, "GSM5936453 r1", "0:8 1:28 2:55", "A:4264761201;C:2967126758;G:3075434435;T:3878445482;N:9914284", 8, 28, 55, null, 4264761201, 2967126758, 3075434435, 3878445482, 9914284, "SRX14395873", "SRS12205980", "SRA1392368", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", 1, 0.9248, null, 0.16768, null, 0.81586, null, 0.61578, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2022-03-07", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [68955, "SRR18254624", "SRX14395873", "SRS12205980", "SRP362863", "PRJNA813520", "Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia", "GSE198044", "Transcriptome Analysis", "The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors  neuroepithelial cells NECs. Although the structure  function and development of the gill have been studied extensively  transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology  we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish  acclimated to 14 days of normoxia and hypoxia. Overall  approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill  including NECs  neurons  pavement cells  endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2  encoding vesicular monoamine transporter  and showed highly differential expressions of tph1a  sv2  and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.", null, "pubmed:35710785", null, "Gill tissue   14d normoxia", "GSM5936453", null, "tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of normoxia", "Gill tissue   14d normoxia", "Raw sequencing data were processed using the CellRanger v5.0.0  10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly  plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function  and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell  and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder  assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA  and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data  SC  files and MULTI seq barcodes  barcode  files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.", "Distal gill filament", null, "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3\u2019 Assay. cDNA synthesis and library construction were carried out according to the manufacturer\u2019s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "genotype:ETvmat2:GFP|treatment:14 days of normoxia", "GSM5936453", "GSM5936453: Gill tissue   14d normoxia; Danio rerio; RNA Seq", "GSM5936453 r1", "GSM5936453", "1", "Distal filaments of gills were trimmed off  trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP362863", null, "loader:fastq load.py", "H1_Barcode_I1.fastq.gz H1_Barcode_R1.fastq.gz H1_Barcode_R2.fastq.gz", "fastq fastq fastq", 1333671703.0, 14655733.0, "GSM5936453 r2", "0:8 1:28 2:55", "A:599872306;C:66845042;G:83153279;T:55613709;N:580979", 8, 28, 55, null, 599872306, 66845042, 83153279, 55613709, 580979, "SRX14395873", "SRS12205980", "SRA1392368", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", "Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)", 1, 0.55243, null, 0.52271, null, 0.99935, null, 0.18823, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2022-03-07", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [74860, "SRR24049049", "SRX19850769", "SRS17208523", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "gill", "GSM7139010", null, "source name:gill|tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "gill", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "gill", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139010", "GSM7139010: gill; Danio rerio; RNA Seq", "GSM7139010 r1", "GSM7139010", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "gill_S1_L001_R1_001.fastq.gz gill_S1_L001_R2_001.fastq.gz", "fastq fastq", 49740465600.0, 165801552.0, "GSM7139010 r1", "0:150 1:150", "A:14168526053;C:8143975613;G:7123512387;T:20303388875;N:1062672", 150, 150, null, null, 14168526053, 8143975613, 7123512387, 20303388875, 1062672, "SRX19850769", "SRS17208523", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.05561, 0.86477, 0.01613, 0.19757, 0.9795, 0.80332, 0.6328, 0.57752, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Gill", "Respiratory System"], [74861, "SRR24049050", "SRX19850769", "SRS17208523", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "gill", "GSM7139010", null, "source name:gill|tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "gill", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "gill", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139010", "GSM7139010: gill; Danio rerio; RNA Seq", "GSM7139010 r1", "GSM7139010", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "gill_S1_L002_R1_001.fastq.gz gill_S1_L002_R2_001.fastq.gz", "fastq fastq", 48791248200.0, 162637494.0, "GSM7139010 r2", "0:150 1:150", "A:13890110368;C:7996697725;G:6992135962;T:19911258999;N:1045146", 150, 150, null, null, 13890110368, 7996697725, 6992135962, 19911258999, 1045146, "SRX19850769", "SRS17208523", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.05401, 0.86634, 0.01505, 0.19619, 0.97926, 0.8016, 0.65268, 0.56185, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Gill", "Respiratory System"], [74862, "SRR24049051", "SRX19850769", "SRS17208523", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "gill", "GSM7139010", null, "source name:gill|tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "gill", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "gill", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139010", "GSM7139010: gill; Danio rerio; RNA Seq", "GSM7139010 r1", "GSM7139010", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "gill_S1_L003_R1_001.fastq.gz gill_S1_L003_R2_001.fastq.gz", "fastq fastq", 62195663700.0, 207318879.0, "GSM7139010 r3", "0:150 1:150", "A:17704771045;C:10195938294;G:8920806416;T:25372821603;N:1326342", 150, 150, null, null, 17704771045, 10195938294, 8920806416, 25372821603, 1326342, "SRX19850769", "SRS17208523", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.05432, 0.86647, 0.0151, 0.19691, 0.9796, 0.80249, 0.62606, 0.57366, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Gill", "Respiratory System"], [74863, "SRR24049052", "SRX19850769", "SRS17208523", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "gill", "GSM7139010", null, "source name:gill|tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "gill", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "gill", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:gill|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139010", "GSM7139010: gill; Danio rerio; RNA Seq", "GSM7139010 r1", "GSM7139010", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "gill_S1_L004_R1_001.fastq.gz gill_S1_L004_R2_001.fastq.gz", "fastq fastq", 51763506000.0, 172545020.0, "GSM7139010 r4", "0:150 1:150", "A:14745588522;C:8480879159;G:7413528516;T:21122400441;N:1109362", 150, 150, null, null, 14745588522, 8480879159, 7413528516, 21122400441, 1109362, "SRX19850769", "SRS17208523", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.05407, 0.86609, 0.01509, 0.19629, 0.97948, 0.80213, 0.62081, 0.58257, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Gill", "Respiratory System"]], "truncated": false, "filtered_table_rows_count": 10, "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", "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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"technology\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "10x", "p1": "Respiratory System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Adult", "label": "Adult", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&devstage_curation=Undetermined", "selected": false}, {"value": "Adult", "label": "Adult", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "Respiratory System", "label": "Respiratory System", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "Gill", "label": "Gill", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System&tissue_curation=Gill", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=10x&tissue_curation_coarse=Respiratory+System", "results": [{"value": "10x", "label": "10x", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation_coarse=Respiratory+System", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 72.53916600166121}