metadata: run_metadata: 10 rows where technology = "10x" and tissue_curation

10 rows where technology = "10x" and tissue_curation_coarse = "Respiratory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
68950	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.	pubmed:35710785	Gill tissue combined normoxia and hypoxia	GSM5936455	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	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’ 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.	genotype:ETvmat2:GFP\|treatment:normoxia and hypoxia samples combined	GSM5936455	GSM5936455: Gill tissue combined normoxia and hypoxia; Danio rerio; RNA Seq	GSM5936455 r1	GSM5936455	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	loader:fastq load.py	HN_SC_I1.fastq.gz HN_SC_R1.fastq.gz HN_SC_R2.fastq.gz	fastq fastq fastq	20585326398.0	226212378.0	GSM5936455 r1	0:8 1:28 2:55	A:3704476968;C:2664002498;G:2831788454;T:3232756993;N:8655877	8	28	55	3704476968	2664002498	2831788454	3232756993	8655877	SRX14395875	SRS12205981	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	0.92742		0.15723		0.83011		0.68192		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
68951	68951	SRR18254620	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.	pubmed:35710785	Gill tissue combined normoxia and hypoxia	GSM5936455	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	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’ 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.	genotype:ETvmat2:GFP\|treatment:normoxia and hypoxia samples combined	GSM5936455	GSM5936455: Gill tissue combined normoxia and hypoxia; Danio rerio; RNA Seq	GSM5936455 r1	GSM5936455	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	loader:fastq load.py	HN_Barcode_I1.fastq.gz HN_Barcode_R1.fastq.gz HN_Barcode_R2.fastq.gz	fastq fastq fastq	1029719145.0	11315595.0	GSM5936455 r2	0:8 1:28 2:55	A:465061193;C:46504427;G:62910508;T:47445353;N:436244	8	28	55	465061193	46504427	62910508	47445353	436244	SRX14395875	SRS12205981	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	0.56414		0.53829		0.99977		0.11976		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
68952	68952	SRR18254621	SRX14395874	SRS12205982	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.	pubmed:35710785	Gill tissue 14d hypoxia	GSM5936454	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	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’ 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.	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	loader:fastq load.py	N1_SC_I1.fastq.gz N1_SC_R1.fastq.gz N1_SC_R2.fastq.gz	fastq fastq fastq	20495108725.0	225220975.0	GSM5936454 r1	0:8 1:28 2:55	A:3710830156;C:2666739789;G:2832783659;T:3168227781;N:8572240	8	28	55	3710830156	2666739789	2832783659	3168227781	8572240	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	0.92266		0.14929		0.83849		0.61082		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
68953	68953	SRR18254622	SRX14395874	SRS12205982	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.	pubmed:35710785	Gill tissue 14d hypoxia	GSM5936454	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	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’ 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.	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	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	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		0.54862		0.99973		0.06569		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
68954	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.	pubmed:35710785	Gill tissue 14d normoxia	GSM5936453	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	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’ 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.	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	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	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		0.16768		0.81586		0.61578		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
68955	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.	pubmed:35710785	Gill tissue 14d normoxia	GSM5936453	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	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’ 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.	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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP362863	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	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		0.52271		0.99935		0.18823		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System
74860	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	pubmed:37453064	gill	GSM7139010	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	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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		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	China	2023-04-03	Adult	Adult	Gill	Respiratory System
74861	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	pubmed:37453064	gill	GSM7139010	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	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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		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	China	2023-04-03	Adult	Adult	Gill	Respiratory System
74862	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	pubmed:37453064	gill	GSM7139010	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	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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		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	China	2023-04-03	Adult	Adult	Gill	Respiratory System
74863	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	pubmed:37453064	gill	GSM7139010	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	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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		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	China	2023-04-03	Adult	Adult	Gill	Respiratory System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;