rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 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,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 52249,SRR9050626,SRX5827017,SRS4754831,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2,GSM3764573,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.,cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764573,GSM3764573: Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2; Danio rerio; RNA Seq,GSM3764573,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo6_possorted_genome_bam.bam,10X Genomics bam file,7642585251.0,134080443.0,GSM3764573 r1,0:57,A:2330102138;C:1530481079;G:1741129436;T:2036914417;N:3958181,57,,,,2330102138,1530481079,1741129436,2036914417,3958181,SRX5827017,SRS4754831,SRA886020,GEO,"Biology, University of Virginia",1,0.92859,,0.20322,,0.83019,,0.51386,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure 52255,SRR9050620,SRX5827011,SRS4754825,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2,GSM3764567,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.,cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,GSM3764567,GSM3764567: Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2; Danio rerio; RNA Seq,GSM3764567,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu5_possorted_genome_bam.bam,10X Genomics bam file,7562050749.0,132667557.0,GSM3764567 r1,0:57,A:2291130941;C:1508834109;G:1752506997;T:2005478206;N:4100496,57,,,,2291130941,1508834109,1752506997,2005478206,4100496,SRX5827011,SRS4754825,SRA886020,GEO,"Biology, University of Virginia",1,0.92351,,0.19606,,0.82913,,0.5204,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure 67321,SRR17117603,SRX13302172,SRS11213397,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day10,GSM5714340,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:10,KIT Day10,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:10,GSM5714340,GSM5714340: KIT Day10; Danio rerio; RNA Seq,GSM5714340 r1,GSM5714340,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD10_possorted_genome_bam.bam,10X Genomics bam file,13520056900.0,270401138.0,GSM5714340 r1,0:50,A:4003001263;C:2787125304;G:3034885371;T:3692995124;N:2049838,50,,,,4003001263,2787125304,3034885371,3692995124,2049838,SRX13302172,SRS11213397,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.89988,,0.15778,,0.81779,,0.55873,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67322,SRR17117604,SRX13302171,SRS11213396,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day5,GSM5714339,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:5,KIT Day5,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:5,GSM5714339,GSM5714339: KIT Day5; Danio rerio; RNA Seq,GSM5714339 r1,GSM5714339,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD5_possorted_genome_bam.bam,10X Genomics bam file,15339323300.0,306786466.0,GSM5714339 r1,0:50,A:4515134365;C:3259123747;G:3665791919;T:3898089485;N:1183784,50,,,,4515134365,3259123747,3665791919,3898089485,1183784,SRX13302171,SRS11213396,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90243,,0.15706,,0.80507,,0.59995,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67323,SRR17117605,SRX13302170,SRS11213395,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day3 2,GSM5714338,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3,KIT Day3 2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:3,GSM5714338,GSM5714338: KIT Day3 2; Danio rerio; RNA Seq,GSM5714338 r1,GSM5714338,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD3B_possorted_genome_bam.bam,10X Genomics bam file,7025134450.0,140502689.0,GSM5714338 r1,0:50,A:2061820993;C:1482027410;G:1665199726;T:1810366819;N:5719502,50,,,,2061820993,1482027410,1665199726,1810366819,5719502,SRX13302170,SRS11213395,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90656,,0.17308,,0.80975,,0.61461,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67324,SRR17117606,SRX13302169,SRS11213394,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day3 1,GSM5714337,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3,KIT Day3 1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:3,GSM5714337,GSM5714337: KIT Day3 1; Danio rerio; RNA Seq,GSM5714337 r1,GSM5714337,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD3A_possorted_genome_bam.bam,10X Genomics bam file,12309733350.0,246194667.0,GSM5714337 r1,0:50,A:3671780931;C:2604474006;G:3028253002;T:3001177496;N:4047915,50,,,,3671780931,2604474006,3028253002,3001177496,4047915,SRX13302169,SRS11213394,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.8991,,0.14599,,0.82347,,0.59507,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67325,SRR17117607,SRX13302168,SRS11213393,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day2,GSM5714336,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:2,KIT Day2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:2,GSM5714336,GSM5714336: KIT Day2; Danio rerio; RNA Seq,GSM5714336 r1,GSM5714336,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD2_possorted_genome_bam.bam,10X Genomics bam file,12734582200.0,254691644.0,GSM5714336 r1,0:50,A:3752064713;C:2645000864;G:2866879156;T:3468673547;N:1963920,50,,,,3752064713,2645000864,2866879156,3468673547,1963920,SRX13302168,SRS11213393,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.9007,,0.15094,,0.82601,,0.58222,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67326,SRR17117608,SRX13302167,SRS11213392,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day1,GSM5714335,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:1,KIT Day1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:1,GSM5714335,GSM5714335: KIT Day1; Danio rerio; RNA Seq,GSM5714335 r1,GSM5714335,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD1_possorted_genome_bam.bam,10X Genomics bam file,11105860850.0,222117217.0,GSM5714335 r1,0:50,A:3280343742;C:2367594246;G:2631026655;T:2823244720;N:3651487,50,,,,3280343742,2367594246,2631026655,2823244720,3651487,SRX13302167,SRS11213392,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.91294,,0.1651,,0.81592,,0.60997,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67327,SRR17117609,SRX13302166,SRS11213391,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT day x,GSM5714334,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:0,KIT day x,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:0,GSM5714334,GSM5714334: KIT day x; Danio rerio; RNA Seq,GSM5714334 r1,GSM5714334,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD0_possorted_genome_bam.bam,10X Genomics bam file,8896963450.0,177939269.0,GSM5714334 r1,0:50,A:2644408729;C:1877280130;G:2120951498;T:2253636691;N:686402,50,,,,2644408729,1877280130,2120951498,2253636691,686402,SRX13302166,SRS11213391,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90601,,0.17428,,0.8144,,0.6019,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67328,SRR17117610,SRX13302165,SRS11213390,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day10,GSM5714333,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:10,WT Day10,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:10,GSM5714333,GSM5714333: WT Day10; Danio rerio; RNA Seq,GSM5714333 r1,GSM5714333,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD10_possorted_genome_bam.bam,10X Genomics bam file,12279427400.0,245588548.0,GSM5714333 r1,0:50,A:3639861301;C:2609067706;G:2996068551;T:3030567477;N:3862365,50,,,,3639861301,2609067706,2996068551,3030567477,3862365,SRX13302165,SRS11213390,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90407,,0.15949,,0.83019,,0.59401,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67329,SRR17117611,SRX13302164,SRS11213389,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day5,GSM5714332,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:5,WT Day5,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:5,GSM5714332,GSM5714332: WT Day5; Danio rerio; RNA Seq,GSM5714332 r1,GSM5714332,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD5_possorted_genome_bam.bam,10X Genomics bam file,8474510800.0,169490216.0,GSM5714332 r1,0:50,A:2564658874;C:1701773199;G:1897587120;T:2308201539;N:2290068,50,,,,2564658874,1701773199,1897587120,2308201539,2290068,SRX13302164,SRS11213389,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.89752,,0.17262,,0.8115,,0.6036,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67330,SRR17117612,SRX13302163,SRS11213388,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day3,GSM5714331,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:3,WT Day3,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:3,GSM5714331,GSM5714331: WT Day3; Danio rerio; RNA Seq,GSM5714331 r1,GSM5714331,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD3_possorted_genome_bam.bam,10X Genomics bam file,9051704300.0,181034086.0,GSM5714331 r1,0:50,A:2665138947;C:1946161834;G:2211744115;T:2225805018;N:2854386,50,,,,2665138947,1946161834,2211744115,2225805018,2854386,SRX13302163,SRS11213388,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90675,,0.14473,,0.81884,,0.58208,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67331,SRR17117613,SRX13302162,SRS11213387,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day2,GSM5714330,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:2,WT Day2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:2,GSM5714330,GSM5714330: WT Day2; Danio rerio; RNA Seq,GSM5714330 r1,GSM5714330,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD2_possorted_genome_bam.bam,10X Genomics bam file,14707462000.0,294149240.0,GSM5714330 r1,0:50,A:4299212743;C:3141543121;G:3608335320;T:3651134459;N:7236357,50,,,,4299212743,3141543121,3608335320,3651134459,7236357,SRX13302162,SRS11213387,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90948,,0.15,,0.81986,,0.58797,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67332,SRR17117614,SRX13302161,SRS11213386,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day1,GSM5714329,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:1,WT Day1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:1,GSM5714329,GSM5714329: WT Day1; Danio rerio; RNA Seq,GSM5714329 r1,GSM5714329,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD1_possorted_genome_bam.bam,10X Genomics bam file,11285903150.0,225718063.0,GSM5714329 r1,0:50,A:3319310923;C:2416106902;G:2709775130;T:2835193792;N:5516403,50,,,,3319310923,2416106902,2709775130,2835193792,5516403,SRX13302161,SRS11213386,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90815,,0.15237,,0.82181,,0.57459,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67333,SRR17117615,SRX13302160,SRS11213385,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT day x 2,GSM5714328,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0,WT day x 2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:0,GSM5714328,GSM5714328: WT day x 2; Danio rerio; RNA Seq,GSM5714328 r1,GSM5714328,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD0B_possorted_genome_bam.bam,10X Genomics bam file,6680383400.0,133607668.0,GSM5714328 r1,0:50,A:2032360836;C:1342388936;G:1478261391;T:1825537806;N:1834431,50,,,,2032360836,1342388936,1478261391,1825537806,1834431,SRX13302160,SRS11213385,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90381,,0.1609,,0.81813,,0.61231,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 67334,SRR17117616,SRX13302159,SRS11213384,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT day x 1,GSM5714327,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0,WT day x 1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:0,GSM5714327,GSM5714327: WT day x 1; Danio rerio; RNA Seq,GSM5714327 r1,GSM5714327,1,Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD0A_possorted_genome_bam.bam,10X Genomics bam file,7628491300.0,152569826.0,GSM5714327 r1,0:50,A:2377995758;C:1521202402;G:1696947530;T:2030231260;N:2114350,50,,,,2377995758,1521202402,1696947530,2030231260,2114350,SRX13302159,SRS11213384,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90188,,0.1668,,0.82154,,0.599,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure 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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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