metadata: run_metadata: 18 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "10x" and tissue

18 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "10x" and tissue_curation = "Skin"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33892	33892	SRR30866052	SRX26263961	SRS22803217	SRP536276	PRJNA1168147	Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq]	GSE278654	Transcriptome Analysis	Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.			m4b mut	GSM8552316	tissue:melanocytes\|cell type:melanocytes\|age:36 hpf\|genotype:mgat4b mutant\|treatment:No\|geo loc name:missing\|collection date:missing	m4b mut	Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files	melanocytes	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction	cell type:melanocytes\|age:36 hpf\|genotype:mgat4b mutant\|treatment:No	GSM8552316	GSM8552316: m4b mut; Danio rerio; RNA Seq	GSM8552316 r1	GSM8552316	1	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP536276	loader:fastq load.py	m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	18274385040.0	132423080.0	GSM8552316 r1	0:10 1:10 2:28 3:90	A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975	10	10	28	90	3788703303	2355223955	2645521958	3126630009	1997975	SRX26263961	SRS22803217	SRA1984944	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB												B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2024-10-02	Pharyngula	Embryo	Skin	Surface Structure
33893	33893	SRR30866053	SRX26263960	SRS22803216	SRP536276	PRJNA1168147	Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq]	GSE278654	Transcriptome Analysis	Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.			Control	GSM8552315	tissue:melanocytes\|cell type:melanocytes\|age:36 hpf\|genotype:control\|treatment:No\|geo loc name:missing\|collection date:missing	Control	Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files	melanocytes	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction	cell type:melanocytes\|age:36 hpf\|genotype:control\|treatment:No	GSM8552315	GSM8552315: Control; Danio rerio; RNA Seq	GSM8552315 r1	GSM8552315	1	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP536276	loader:fastq load.py	con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	15825218034.0	114675493.0	GSM8552315 r1	0:10 1:10 2:28 3:90	A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229	10	10	28	90	3074750870	2137365424	2401965854	2704984993	1727229	SRX26263960	SRS22803216	SRA1984944	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB												B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2024-10-02	Pharyngula	Embryo	Skin	Surface Structure
69558	69558	SRR18901602	SRX14979859	SRS12729750	SRP371883	PRJNA831276	Lipid droplets are a metabolic vulnerability in melanoma	GSE201378	Transcriptome Analysis	Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma		pubmed:37268606	TEAZ scRNAseq	GSM6062264	source name:Skin\|tissue:Skin\|cell type:melanoma	TEAZ scRNAseq	Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11	Skin	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	tissue:Skin\|cell type:melanoma	GSM6062264	GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq	GSM6062264 r1	GSM6062264	1	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP371883	loader:fastq load.py	2544_PTEN_combined_IGO_11963_4_S2_L001_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L001_R2_001.fastq.gz	fastq fastq	9314576760.0	77621473.0	GSM6062264 r1	0:29 1:91	A:2571624849;C:2103171866;G:2248508025;T:2390911966;N:360054	29	91			2571624849	2103171866	2248508025	2390911966	360054	SRX14979859	SRS12729750	SRA1408865	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	2	0.00434	0.8777	0.00177	0.14429	0.99253	0.78492	0.35282	0.53036	29	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-04-23	Undetermined	Undetermined	Skin	Surface Structure
69559	69559	SRR18901603	SRX14979859	SRS12729750	SRP371883	PRJNA831276	Lipid droplets are a metabolic vulnerability in melanoma	GSE201378	Transcriptome Analysis	Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma		pubmed:37268606	TEAZ scRNAseq	GSM6062264	source name:Skin\|tissue:Skin\|cell type:melanoma	TEAZ scRNAseq	Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11	Skin	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	tissue:Skin\|cell type:melanoma	GSM6062264	GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq	GSM6062264 r1	GSM6062264	1	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP371883	loader:fastq load.py	2544_PTEN_combined_IGO_11963_4_S2_L002_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L002_R2_001.fastq.gz	fastq fastq	9122357880.0	76019649.0	GSM6062264 r2	0:29 1:91	A:2521047948;C:2056950129;G:2200048731;T:2343919901;N:391171	29	91			2521047948	2056950129	2200048731	2343919901	391171	SRX14979859	SRS12729750	SRA1408865	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	2	0.00471	0.87992	0.00196	0.14374	0.99255	0.78476	0.35593	0.54484	29	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-04-23	Undetermined	Undetermined	Skin	Surface Structure
69560	69560	SRR18901604	SRX14979859	SRS12729750	SRP371883	PRJNA831276	Lipid droplets are a metabolic vulnerability in melanoma	GSE201378	Transcriptome Analysis	Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma		pubmed:37268606	TEAZ scRNAseq	GSM6062264	source name:Skin\|tissue:Skin\|cell type:melanoma	TEAZ scRNAseq	Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11	Skin	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	tissue:Skin\|cell type:melanoma	GSM6062264	GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq	GSM6062264 r1	GSM6062264	1	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP371883	loader:fastq load.py	2544_PTEN_combined_IGO_11963_4_S2_L003_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L003_R2_001.fastq.gz	fastq fastq	9307586160.0	77563218.0	GSM6062264 r3	0:29 1:91	A:2569072609;C:2102732051;G:2247036264;T:2388393636;N:351600	29	91			2569072609	2102732051	2247036264	2388393636	351600	SRX14979859	SRS12729750	SRA1408865	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	2	0.00429	0.87889	0.00178	0.1429	0.99271	0.78589	0.35728	0.54587	29	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-04-23	Undetermined	Undetermined	Skin	Surface Structure
69561	69561	SRR18901605	SRX14979859	SRS12729750	SRP371883	PRJNA831276	Lipid droplets are a metabolic vulnerability in melanoma	GSE201378	Transcriptome Analysis	Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma		pubmed:37268606	TEAZ scRNAseq	GSM6062264	source name:Skin\|tissue:Skin\|cell type:melanoma	TEAZ scRNAseq	Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11	Skin	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	tissue:Skin\|cell type:melanoma	GSM6062264	GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq	GSM6062264 r1	GSM6062264	1	Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP371883	loader:fastq load.py	2544_PTEN_combined_IGO_11963_4_S2_L004_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L004_R2_001.fastq.gz	fastq fastq	9382270920.0	78185591.0	GSM6062264 r4	0:29 1:91	A:2591803792;C:2116313097;G:2264892157;T:2408930364;N:331510	29	91			2591803792	2116313097	2264892157	2408930364	331510	SRX14979859	SRS12729750	SRA1408865	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center	2	0.00445	0.87912	0.00184	0.14625	0.99287	0.78573	0.37029	0.5207	29	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-04-23	Undetermined	Undetermined	Skin	Surface Structure
74804	74804	SRR24043073	SRX19845029	SRS17204126	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi2	GSM7135751	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi2	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135751	GSM7135751: epi2; Danio rerio; RNA Seq	GSM7135751 r1	GSM7135751	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi2_S1_L001_R1_001.fastq.gz epi2_S1_L001_R2_001.fastq.gz	fastq fastq	53272554600.0	177575182.0	GSM7135751 r1	0:150 1:150	A:22273594251;C:9171565164;G:8634752690;T:13192111379;N:531116	150	150			22273594251	9171565164	8634752690	13192111379	531116	SRX19845029	SRS17204126	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87992	0.0	0.19142	1.0	0.8143		0.56327	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74805	74805	SRR24043074	SRX19845029	SRS17204126	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi2	GSM7135751	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi2	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135751	GSM7135751: epi2; Danio rerio; RNA Seq	GSM7135751 r1	GSM7135751	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi2_S1_L002_R1_001.fastq.gz epi2_S1_L002_R2_001.fastq.gz	fastq fastq	48364190400.0	161213968.0	GSM7135751 r2	0:150 1:150	A:20333401181;C:8352480913;G:7827379016;T:11850446550;N:482740	150	150			20333401181	8352480913	7827379016	11850446550	482740	SRX19845029	SRS17204126	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87888	0.0	0.19128	1.0	0.81306		0.55856	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74806	74806	SRR24043075	SRX19845029	SRS17204126	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi2	GSM7135751	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi2	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135751	GSM7135751: epi2; Danio rerio; RNA Seq	GSM7135751 r1	GSM7135751	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi2_S1_L003_R1_001.fastq.gz epi2_S1_L003_R2_001.fastq.gz	fastq fastq	51045865200.0	170152884.0	GSM7135751 r3	0:150 1:150	A:21367712192;C:8808280025;G:8280670496;T:12588694433;N:508054	150	150			21367712192	8808280025	8280670496	12588694433	508054	SRX19845029	SRS17204126	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87796	0.0	0.18975	1.0	0.81631		0.56084	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74807	74807	SRR24043076	SRX19845029	SRS17204126	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi2	GSM7135751	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi2	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135751	GSM7135751: epi2; Danio rerio; RNA Seq	GSM7135751 r1	GSM7135751	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi2_S1_L004_R1_001.fastq.gz epi2_S1_L004_R2_001.fastq.gz	fastq fastq	44581454400.0	148604848.0	GSM7135751 r4	0:150 1:150	A:18688290657;C:7694495772;G:7225584087;T:10972642933;N:440951	150	150			18688290657	7694495772	7225584087	10972642933	440951	SRX19845029	SRS17204126	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.88007	0.0	0.19008	1.0	0.81489		0.55702	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74808	74808	SRR24043077	SRX19845028	SRS17204127	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi1	GSM7135750	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi1	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135750	GSM7135750: epi1; Danio rerio; RNA Seq	GSM7135750 r1	GSM7135750	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi1_S1_L001_R1_001.fastq.gz epi1_S1_L001_R2_001.fastq.gz	fastq fastq	45973209600.0	153244032.0	GSM7135750 r1	0:150 1:150	A:19246011620;C:7887556815;G:7422189358;T:11416995932;N:455875	150	150			19246011620	7887556815	7422189358	11416995932	455875	SRX19845028	SRS17204127	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.8759	0.0	0.1936	1.0	0.81422		0.56458	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74809	74809	SRR24043078	SRX19845028	SRS17204127	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi1	GSM7135750	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi1	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135750	GSM7135750: epi1; Danio rerio; RNA Seq	GSM7135750 r1	GSM7135750	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi1_S1_L002_R1_001.fastq.gz epi1_S1_L002_R2_001.fastq.gz	fastq fastq	53460624000.0	178202080.0	GSM7135750 r2	0:150 1:150	A:22432826189;C:9167346004;G:8618412138;T:13241507017;N:532652	150	150			22432826189	9167346004	8618412138	13241507017	532652	SRX19845028	SRS17204127	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87765	0.0	0.1928	1.0	0.81221		0.56399	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74810	74810	SRR24043079	SRX19845028	SRS17204127	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi1	GSM7135750	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi1	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135750	GSM7135750: epi1; Danio rerio; RNA Seq	GSM7135750 r1	GSM7135750	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi1_S1_L003_R1_001.fastq.gz epi1_S1_L003_R2_001.fastq.gz	fastq fastq	44119071900.0	147063573.0	GSM7135750 r3	0:150 1:150	A:18526609900;C:7587649387;G:7122121937;T:10882250695;N:439981	150	150			18526609900	7587649387	7122121937	10882250695	439981	SRX19845028	SRS17204127	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87634	0.0	0.19229	1.0	0.81276		0.56294	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74811	74811	SRR24043080	SRX19845028	SRS17204127	SRP430482	PRJNA951388	single cell RNA sequencing analysis of metaphocytes and epidermal cells	GSE228737	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish	parent bioproject:PRJNA951389	pubmed:37148242	epi1	GSM7135750	source name:epidermis\|tissue:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	epi1	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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files	epidermis	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis\|development stage:6 mpf\|cell type:spic:EGFP+ and singlet cells\|strain:Tgspic:EGFP\|genotype:WT	GSM7135750	GSM7135750: epi1; Danio rerio; RNA Seq	GSM7135750 r1	GSM7135750	1	Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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	SRP430482		epi1_S1_L004_R1_001.fastq.gz epi1_S1_L004_R2_001.fastq.gz	fastq fastq	51145329000.0	170484430.0	GSM7135750 r4	0:150 1:150	A:21450511349;C:8780885548;G:8246807762;T:12666616586;N:507755	150	150			21450511349	8780885548	8246807762	12666616586	507755	SRX19845028	SRS17204127	SRA1614473	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.0	0.87725	0.0	0.19191	1.0	0.81276		0.56272	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-02	Adult	Adult	Skin	Surface Structure
74864	74864	SRR24049053	SRX19850768	SRS17208522	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	epidermis	GSM7139009	source name:epidermis\|tissue:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT\|geo loc name:missing\|collection date:missing	epidermis	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	epidermis	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:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT	GSM7139009	GSM7139009: epidermis; Danio rerio; RNA Seq	GSM7139009 r1	GSM7139009	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		epidermis_S1_L001_R1_001.fastq.gz epidermis_S1_L001_R2_001.fastq.gz	fastq fastq	51217913700.0	170726379.0	GSM7139009 r1	0:150 1:150	A:14615897142;C:8371630215;G:7297500033;T:20931789086;N:1097224	150	150			14615897142	8371630215	7297500033	20931789086	1097224	SRX19850768	SRS17208522	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	0.06036	0.85549	0.01635	0.2133	0.98001	0.81564	0.66191	0.6026	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	Skin	Surface Structure
74865	74865	SRR24049054	SRX19850768	SRS17208522	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	epidermis	GSM7139009	source name:epidermis\|tissue:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT\|geo loc name:missing\|collection date:missing	epidermis	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	epidermis	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:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT	GSM7139009	GSM7139009: epidermis; Danio rerio; RNA Seq	GSM7139009 r1	GSM7139009	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		epidermis_S1_L002_R1_001.fastq.gz epidermis_S1_L002_R2_001.fastq.gz	fastq fastq	11621169000.0	38737230.0	GSM7139009 r2	0:150 1:150	A:3309444788;C:1902982764;G:1659558855;T:4748933974;N:248619	150	150			3309444788	1902982764	1659558855	4748933974	248619	SRX19850768	SRS17208522	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	0.06171	0.85494	0.0158	0.21181	0.98037	0.81558	0.65361	0.59223	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	Skin	Surface Structure
74866	74866	SRR24049055	SRX19850768	SRS17208522	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	epidermis	GSM7139009	source name:epidermis\|tissue:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT\|geo loc name:missing\|collection date:missing	epidermis	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	epidermis	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:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT	GSM7139009	GSM7139009: epidermis; Danio rerio; RNA Seq	GSM7139009 r1	GSM7139009	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		epidermis_S1_L003_R1_001.fastq.gz epidermis_S1_L003_R2_001.fastq.gz	fastq fastq	47730020700.0	159100069.0	GSM7139009 r3	0:150 1:150	A:13610937789;C:7804335610;G:6807692411;T:19506030904;N:1023986	150	150			13610937789	7804335610	6807692411	19506030904	1023986	SRX19850768	SRS17208522	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	0.06245	0.85768	0.01724	0.21301	0.97918	0.81554	0.64857	0.60209	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	Skin	Surface Structure
74867	74867	SRR24049056	SRX19850768	SRS17208522	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	epidermis	GSM7139009	source name:epidermis\|tissue:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT\|geo loc name:missing\|collection date:missing	epidermis	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	epidermis	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:epidermis\|age:6 mpf\|cell type:mpeg1.1+ cells\|strain:Tgmpeg1.1:DsRedx\|genotype:WT	GSM7139009	GSM7139009: epidermis; Danio rerio; RNA Seq	GSM7139009 r1	GSM7139009	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		epidermis_S1_L004_R1_001.fastq.gz epidermis_S1_L004_R2_001.fastq.gz	fastq fastq	52131659700.0	173772199.0	GSM7139009 r4	0:150 1:150	A:14870283464;C:8522177878;G:7429591607;T:21308487629;N:1119122	150	150			14870283464	8522177878	7429591607	21308487629	1119122	SRX19850768	SRS17208522	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	0.05864	0.8548	0.01546	0.21132	0.98092	0.81221	0.66289	0.5878	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	Skin	Surface Structure

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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");;