metadata: run_metadata: 16 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

16 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Skin"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
52249	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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