{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"smartseq\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[51228, "SRR8591752", "SRX5391965", "SRS4379795", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 3", "GSM3612324", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 2", "GSM3612323", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. 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Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612323", "GSM3612323: T cells 2; Danio rerio; RNA Seq", "GSM3612323", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 1", "GSM3612322", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. 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Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612322", "GSM3612322: T cells 1; Danio rerio; RNA Seq", "GSM3612322", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 3", "GSM3612321", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "GSM3612321", "GSM3612321: Neutrophils 3; Danio rerio; RNA Seq", "GSM3612321", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 2", "GSM3612320", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "GSM3612320", "GSM3612320: Neutrophils 2; Danio rerio; RNA Seq", "GSM3612320", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 1", "GSM3612319", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 4", "GSM3612318", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 4", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 3", "GSM3612317", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612317", "GSM3612317: MLCs 3; Danio rerio; RNA Seq", "GSM3612317", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612317", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_3_R1.fq.gz MLCs_3_R2.fq.gz", "fastq fastq", 9768968700.0, 32563229.0, "GSM3612317 r1", "0:150 1:150", "A:2993731360;C:1868928141;G:1920209904;T:2983932349;N:2166946", 150, 150, null, null, 2993731360, 1868928141, 1920209904, 2983932349, 2166946, "SRX5391958", "SRS4379788", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80623, 0.80159, 0.09971, 0.09865, 0.85754, 0.85677, 0.57368, 0.57722, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51236, "SRR8591744", "SRX5391957", "SRS4379787", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 2", "GSM3612316", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612316", "GSM3612316: MLCs 2; Danio rerio; RNA Seq", "GSM3612316", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612316", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_2_R2.fq.gz MLCs_2_R1.fq.gz", "fastq fastq", 13514398200.0, 45047994.0, "GSM3612316 r1", "0:150 1:150", "A:3741759684;C:2708870921;G:2854612129;T:4207496675;N:1658791", 150, 150, null, null, 3741759684, 2708870921, 2854612129, 4207496675, 1658791, "SRX5391957", "SRS4379787", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.85592, 0.84009, 0.10566, 0.10231, 0.85904, 0.86689, 0.46757, 0.54817, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51237, "SRR8591743", "SRX5391956", "SRS4379786", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 1", "GSM3612315", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612315", "GSM3612315: MLCs 1; Danio rerio; RNA Seq", "GSM3612315", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612315", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_1_R1.fq.gz MLCs_1_R2.fq.gz", "fastq fastq", 6037864832.0, 20003506.0, "GSM3612315 r1", "0:150.92 1:150.92", "A:1818516368;C:1085016023;G:1139951931;T:1985307132;N:9073378", 150, 150, null, null, 1818516368, 1085016023, 1139951931, 1985307132, 9073378, "SRX5391956", "SRS4379786", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.74163, 0.65034, 0.20675, 0.17721, 0.85285, 0.87409, 0.66103, 0.66629, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51238, "SRR8591742", "SRX5391955", "SRS4379784", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 3", "GSM3612314", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612314", "GSM3612314: Keratinocytes 3; Danio rerio; RNA Seq", "GSM3612314", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612314", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_3_R1.fq.gz Keratinocytes_3_R2.fq.gz", "fastq fastq", 7155019200.0, 23850064.0, "GSM3612314 r1", "0:150 1:150", "A:2267290727;C:1304084105;G:1335196968;T:2248029844;N:417556", 150, 150, null, null, 2267290727, 1304084105, 1335196968, 2248029844, 417556, "SRX5391955", "SRS4379784", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.77684, 0.75758, 0.12563, 0.12043, 0.87606, 0.87618, 0.63846, 0.64712, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51239, "SRR8591741", "SRX5391954", "SRS4379785", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 2", "GSM3612313", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612313", "GSM3612313: Keratinocytes 2; Danio rerio; RNA Seq", "GSM3612313", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612313", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_2_R1.fq.gz Keratinocytes_2_R2.fq.gz", "fastq fastq", 6456398100.0, 21521327.0, "GSM3612313 r1", "0:150 1:150", "A:2077468795;C:1142603883;G:1144675726;T:2084897858;N:6751838", 150, 150, null, null, 2077468795, 1142603883, 1144675726, 2084897858, 6751838, "SRX5391954", "SRS4379785", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.74005, 0.73114, 0.1187, 0.11653, 0.8604, 0.85985, 0.56777, 0.56778, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51240, "SRR8591740", "SRX5391953", "SRS4379783", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 1", "GSM3612312", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612312", "GSM3612312: Keratinocytes 1; Danio rerio; RNA Seq", "GSM3612312", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612312", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_1_R2.fq.gz Keratinocytes_1_R1.fq.gz", "fastq fastq", 13235365200.0, 44117884.0, "GSM3612312 r1", "0:150 1:150", "A:3733277705;C:2648363624;G:2742826351;T:4109351172;N:1546348", 150, 150, null, null, 3733277705, 2648363624, 2742826351, 4109351172, 1546348, "SRX5391953", "SRS4379783", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.83183, 0.82563, 0.13916, 0.13781, 0.86048, 0.86517, 0.46753, 0.45399, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51241, "SRR8591739", "SRX5391952", "SRS4379782", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 4", "GSM3612311", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 4", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612311", "GSM3612311: cLCs 4; Danio rerio; RNA Seq", "GSM3612311", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612311", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_4_R1.fq.gz cLCs_4_R2.fq.gz", "fastq fastq", 8713251600.0, 29044172.0, "GSM3612311 r1", "0:150 1:150", "A:2637859361;C:1663768374;G:1739990329;T:2671283369;N:350167", 150, 150, null, null, 2637859361, 1663768374, 1739990329, 2671283369, 350167, "SRX5391952", "SRS4379782", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82506, 0.82564, 0.14826, 0.14636, 0.92133, 0.92194, 0.64203, 0.64155, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51242, "SRR8591738", "SRX5391951", "SRS4379781", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 3", "GSM3612310", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612310", "GSM3612310: cLCs 3; Danio rerio; RNA Seq", "GSM3612310", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612310", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_3_R2.fq.gz cLCs_3_R1.fq.gz", "fastq fastq", 8085762300.0, 26952541.0, "GSM3612310 r1", "0:150 1:150", "A:2358914181;C:1670033364;G:1711269394;T:2345255094;N:290267", 150, 150, null, null, 2358914181, 1670033364, 1711269394, 2345255094, 290267, "SRX5391951", "SRS4379781", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80361, 0.80478, 0.06011, 0.06067, 0.90666, 0.90613, 0.43542, 0.42737, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51243, "SRR8591737", "SRX5391950", "SRS4379780", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 2", "GSM3612309", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612309", "GSM3612309: cLCs 2; Danio rerio; RNA Seq", "GSM3612309", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612309", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_2_R2.fq.gz cLCs_2_R1.fq.gz", "fastq fastq", 14035834800.0, 46786116.0, "GSM3612309 r1", "0:150 1:150", "A:3886956713;C:2808123594;G:3002545528;T:4337287271;N:921694", 150, 150, null, null, 3886956713, 2808123594, 3002545528, 4337287271, 921694, "SRX5391950", "SRS4379780", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80521, 0.79346, 0.13916, 0.13314, 0.88061, 0.88872, 0.5212, 0.54523, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51244, "SRR8591736", "SRX5391949", "SRS4379779", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 1", "GSM3612308", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612308", "GSM3612308: cLCs 1; Danio rerio; RNA Seq", "GSM3612308", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612308", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_1_R1.fq.gz cLCs_1_R2.fq.gz", "fastq fastq", 6917825858.0, 22926042.0, "GSM3612308 r1", "0:150.87 1:150.87", "A:2168007671;C:1152140252;G:1228288198;T:2358773829;N:10615908", 150, 150, null, null, 2168007671, 1152140252, 1228288198, 2358773829, 10615908, "SRX5391949", "SRS4379779", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.6965, 0.66301, 0.20956, 0.19509, 0.8521, 0.86218, 0.6102, 0.59061, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [61390, "SRR12708451", "SRX9187386", "SRS7423761", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFN3", "GSM4802478", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFN3", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802478", "GSM4802478: MFN3; Danio rerio; RNA Seq", "GSM4802478", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802478", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFN3_R1_001.fastq.gz MFN3_R2_001.fastq.gz", "fastq fastq", 14558703600.0, 48529012.0, "GSM4802478 r1", "0:150 1:150", "A:3871514784;C:3434394240;G:3331911824;T:3919968300;N:914452", 150, 150, null, null, 3871514784, 3434394240, 3331911824, 3919968300, 914452, "SRX9187386", "SRS7423761", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.89707, 0.89196, 0.05724, 0.05696, 0.75396, 0.75597, 0.43181, 0.41631, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61391, "SRR12708450", "SRX9187385", "SRS7423760", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFG3", "GSM4802477", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFG3", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802477", "GSM4802477: MFG3; Danio rerio; RNA Seq", "GSM4802477", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802477", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFG3_R1_001.fastq.gz MFG3_R2_001.fastq.gz", "fastq fastq", 10045323900.0, 33484413.0, "GSM4802477 r1", "0:150 1:150", "A:2619233046;C:2425417526;G:2312268655;T:2687771920;N:632753", 150, 150, null, null, 2619233046, 2425417526, 2312268655, 2687771920, 632753, "SRX9187385", "SRS7423760", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.90365, 0.90046, 0.06439, 0.06489, 0.75436, 0.75641, 0.54634, 0.54693, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61394, "SRR12708447", "SRX9187382", "SRS7423757", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFN3", "GSM4802474", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFN3", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802474", "GSM4802474: XFN3; Danio rerio; RNA Seq", "GSM4802474", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFN3_R1_001.fastq.gz XFN3_R2_001.fastq.gz", "fastq fastq", 11204873700.0, 37349579.0, "GSM4802474 r1", "0:150 1:150", "A:2943394483;C:2667470839;G:2579644073;T:3013655182;N:709123", 150, 150, null, null, 2943394483, 2667470839, 2579644073, 3013655182, 709123, "SRX9187382", "SRS7423757", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.90055, 0.89407, 0.05457, 0.05489, 0.74247, 0.746, 0.48492, 0.48602, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61395, "SRR12708446", "SRX9187381", "SRS7423756", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFG3", "GSM4802473", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFG3", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802473", "GSM4802473: XFG3; Danio rerio; RNA Seq", "GSM4802473", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFG3_R1_001.fastq.gz XFG3_R2_001.fastq.gz", "fastq fastq", 11212083000.0, 37373610.0, "GSM4802473 r1", "0:150 1:150", "A:2979985262;C:2652925544;G:2513147966;T:3065318302;N:705926", 150, 150, null, null, 2979985262, 2652925544, 2513147966, 3065318302, 705926, "SRX9187381", "SRS7423756", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.9056, 0.89972, 0.06159, 0.06165, 0.74194, 0.74602, 0.49523, 0.44889, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61398, "SRR12708443", "SRX9187378", "SRS7423753", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFN2", "GSM4802470", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFN2", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802470", "GSM4802470: MFN2; Danio rerio; RNA Seq", "GSM4802470", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFN2_R1_001.fastq.gz MFN2_R2_001.fastq.gz", "fastq fastq", 9002969100.0, 30009897.0, "GSM4802470 r1", "0:150 1:150", "A:2383579322;C:2152753900;G:2013843514;T:2452228154;N:564210", 150, 150, null, null, 2383579322, 2152753900, 2013843514, 2452228154, 564210, "SRX9187378", "SRS7423753", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.89613, 0.89129, 0.06896, 0.06936, 0.75235, 0.75659, 0.51059, 0.50763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61399, "SRR12708442", "SRX9187377", "SRS7423752", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFG2", "GSM4802469", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFG2", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802469", "GSM4802469: MFG2; Danio rerio; RNA Seq", "GSM4802469", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFG2_R1_001.fastq.gz MFG2_R2_001.fastq.gz", "fastq fastq", 11893039800.0, 39643466.0, "GSM4802469 r1", "0:150 1:150", "A:3160384920;C:2834257771;G:2698430613;T:3199226169;N:740327", 150, 150, null, null, 3160384920, 2834257771, 2698430613, 3199226169, 740327, "SRX9187377", "SRS7423752", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.90353, 0.89813, 0.06957, 0.06993, 0.75183, 0.75607, 0.46098, 0.51543, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61402, "SRR12708439", "SRX9187374", "SRS7423749", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFN2", "GSM4802466", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFN2", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802466", "GSM4802466: XFN2; Danio rerio; RNA Seq", "GSM4802466", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802466", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFN2_R1_001.fastq.gz XFN2_R2_001.fastq.gz", "fastq fastq", 11313005400.0, 37710018.0, "GSM4802466 r1", "0:150 1:150", "A:2996096346;C:2703585714;G:2550898118;T:3061720444;N:704778", 150, 150, null, null, 2996096346, 2703585714, 2550898118, 3061720444, 704778, "SRX9187374", "SRS7423749", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.88653, 0.88127, 0.06171, 0.06088, 0.74856, 0.75252, 0.51699, 0.51503, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61403, "SRR12708438", "SRX9187373", "SRS7423748", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFG2", "GSM4802465", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFG2", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802465", "GSM4802465: XFG2; Danio rerio; RNA Seq", "GSM4802465", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802465", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFG2_R1_001.fastq.gz XFG2_R2_001.fastq.gz", "fastq fastq", 11921269800.0, 39737566.0, "GSM4802465 r1", "0:150 1:150", "A:3191695537;C:2823855056;G:2636104989;T:3268877243;N:736975", 150, 150, null, null, 3191695537, 2823855056, 2636104989, 3268877243, 736975, "SRX9187373", "SRS7423748", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.89811, 0.89304, 0.06734, 0.0674, 0.7391, 0.74261, 0.51932, 0.45328, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61406, "SRR12708435", "SRX9187370", "SRS7423745", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFN1", "GSM4802462", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFN1", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802462", "GSM4802462: MFN1; Danio rerio; RNA Seq", "GSM4802462", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFN1_R1_001.fastq.gz MFN1_R2_001.fastq.gz", "fastq fastq", 12560283900.0, 41867613.0, "GSM4802462 r1", "0:150 1:150", "A:3295279231;C:3013386640;G:2898979550;T:3351847365;N:791114", 150, 150, null, null, 3295279231, 3013386640, 2898979550, 3351847365, 791114, "SRX9187370", "SRS7423745", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.89681, 0.89104, 0.06566, 0.06589, 0.74272, 0.74791, 0.51645, 0.51902, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61407, "SRR12708434", "SRX9187369", "SRS7423744", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "MFG1", "GSM4802461", null, "tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin", "MFG1", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802461", "GSM4802461: MFG1; Danio rerio; RNA Seq", "GSM4802461", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "MFG1_R1_001.fastq.gz MFG1_R2_001.fastq.gz", "fastq fastq", 11317873500.0, 37726245.0, "GSM4802461 r1", "0:150 1:150", "A:2947830189;C:2733463243;G:2616872694;T:3018996791;N:710583", 150, 150, null, null, 2947830189, 2733463243, 2616872694, 3018996791, 710583, "SRX9187369", "SRS7423744", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.90788, 0.90139, 0.06383, 0.06478, 0.74268, 0.74686, 0.50725, 0.50595, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61410, "SRR12708431", "SRX9187366", "SRS7423741", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFN1", "GSM4802458", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFN1", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ", "GSM4802458", "GSM4802458: XFN1; Danio rerio; RNA Seq", "GSM4802458", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFN1_R1_001.fastq.gz XFN1_R2_001.fastq.gz", "fastq fastq", 11573931900.0, 38579773.0, "GSM4802458 r1", "0:150 1:150", "A:2999184334;C:2801583964;G:2672180906;T:3100254047;N:728649", 150, 150, null, null, 2999184334, 2801583964, 2672180906, 3100254047, 728649, "SRX9187366", "SRS7423741", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.8962, 0.88921, 0.05791, 0.05848, 0.74097, 0.7471, 0.50594, 0.5107, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [61411, "SRR12708430", "SRX9187365", "SRS7423740", "SRP285315", "PRJNA665531", "Bulk RNA seq of fin and body melanocytes and microenvironments", "GSE158538", "Transcriptome Analysis", "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.", null, "pubmed:35355015", null, "XFG1", "GSM4802457", null, "tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin", "XFG1", "md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated", "Zebrafish fins", null, "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", null, "strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+", "GSM4802457", "GSM4802457: XFG1; Danio rerio; RNA Seq", "GSM4802457", null, "1", "Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.", "GEO Accession:GSM4802457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP285315", null, null, "XFG1_R1_001.fastq.gz XFG1_R2_001.fastq.gz", "fastq fastq", 11738198700.0, 39127329.0, "GSM4802457 r1", "0:150 1:150", "A:3083667179;C:2816699592;G:2648683281;T:3188411465;N:737183", 150, 150, null, null, 3083667179, 2816699592, 2648683281, 3188411465, 737183, "SRX9187365", "SRS7423740", "SRA1131319", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.90455, 0.89777, 0.05668, 0.05707, 0.74631, 0.75057, 0.49373, 0.48957, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-09-24", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [64331, "SRR14551653", "SRX10895137", "SRS8987960", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "neuronal 72hpf Sample3", "GSM5315776", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf", "neuronal 72hpf Sample3", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgnbt:dsred|age:72 hpf", "GSM5315776", "GSM5315776: neuronal 72hpf Sample3; Danio rerio; RNA Seq", "GSM5315776", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315776", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "neuronal72_Sample3_R1_001.fastq.gz neuronal72_Sample3_R2_001.fastq.gz", "fastq fastq", 5811578187.0, 19461304.0, "GSM5315776 r1", "0:149.33 1:149.29", "A:1529597778;C:1363449364;G:1361318435;T:1556834579;N:378031", 149, 149, null, null, 1529597778, 1363449364, 1361318435, 1556834579, 378031, "SRX10895137", "SRS8987960", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.86088, 0.86196, 0.09968, 0.09909, 0.76952, 0.77553, 0.47402, 0.46267, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64332, "SRR14551652", "SRX10895136", "SRS8987961", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "neuronal 72hpf Sample2", "GSM5315775", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf", "neuronal 72hpf Sample2", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgnbt:dsred|age:72 hpf", "GSM5315775", "GSM5315775: neuronal 72hpf Sample2; Danio rerio; RNA Seq", "GSM5315775", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315775", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "neuronal72_Sample2_R1_001.fastq.gz neuronal72_Sample2_R2_001.fastq.gz", "fastq fastq", 5330377491.0, 17862084.0, "GSM5315775 r1", "0:149.23 1:149.19", "A:1408165778;C:1247044167;G:1242879903;T:1431943960;N:343683", 149, 149, null, null, 1408165778, 1247044167, 1242879903, 1431943960, 343683, "SRX10895136", "SRS8987961", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.82586, 0.83096, 0.1393, 0.14169, 0.7907, 0.79555, 0.46473, 0.48234, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64333, "SRR14551651", "SRX10895135", "SRS8987956", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "neuronal 72hpf Sample1", "GSM5315774", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf", "neuronal 72hpf Sample1", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgnbt:dsred|age:72 hpf", "GSM5315774", "GSM5315774: neuronal 72hpf Sample1; Danio rerio; RNA Seq", "GSM5315774", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315774", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "neuronal72_Sample1_R1_001.fastq.gz neuronal72_Sample1_R2_001.fastq.gz", "fastq fastq", 7122524050.0, 23888399.0, "GSM5315774 r1", "0:149.11 1:149.05", "A:1867527557;C:1687169064;G:1683673406;T:1883615223;N:538800", 149, 149, null, null, 1867527557, 1687169064, 1683673406, 1883615223, 538800, "SRX10895135", "SRS8987956", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.88793, 0.88809, 0.12727, 0.12826, 0.7486, 0.75635, 0.42346, 0.48977, 149, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64334, "SRR14551650", "SRX10895134", "SRS8987957", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "OPC 72hpf Sample3", "GSM5315773", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf", "OPC 72hpf Sample3", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf", "GSM5315773", "GSM5315773: OPC 72hpf Sample3; Danio rerio; RNA Seq", "GSM5315773", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315773", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "OPC72_Sample3_R1_001.fastq.gz OPC72_Sample3_R2_001.fastq.gz", "fastq fastq", 6630077092.0, 22212439.0, "GSM5315773 r1", "0:149.27 1:149.22", "A:1681054163;C:1589572166;G:1588126414;T:1770833666;N:490683", 149, 149, null, null, 1681054163, 1589572166, 1588126414, 1770833666, 490683, "SRX10895134", "SRS8987957", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.69031, 0.6945, 0.1106, 0.1101, 0.85123, 0.85389, 0.45515, 0.45517, 149, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64335, "SRR14551649", "SRX10895133", "SRS8987958", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "OPC 72hpf Sample2", "GSM5315772", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf", "OPC 72hpf Sample2", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf", "GSM5315772", "GSM5315772: OPC 72hpf Sample2; Danio rerio; RNA Seq", "GSM5315772", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315772", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "OPC72_Sample2_R1_001.fastq.gz OPC72_Sample2_R2_001.fastq.gz", "fastq fastq", 7703607275.0, 25797864.0, "GSM5315772 r1", "0:149.33 1:149.29", "A:2052466926;C:1756697559;G:1751055673;T:2142874669;N:512448", 149, 149, null, null, 2052466926, 1756697559, 1751055673, 2142874669, 512448, "SRX10895133", "SRS8987958", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.78396, 0.7872, 0.15128, 0.15083, 0.80176, 0.8043, 0.47044, 0.47071, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64336, "SRR14551648", "SRX10895132", "SRS8987959", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "OPC 72hpf Sample1", "GSM5315771", null, "tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf", "OPC 72hpf Sample1", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf", "GSM5315771", "GSM5315771: OPC 72hpf Sample1; Danio rerio; RNA Seq", "GSM5315771", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315771", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "OPC72_Sample1_R1_001.fastq.gz OPC72_Sample1_R2_001.fastq.gz", "fastq fastq", 6819055600.0, 22845167.0, "GSM5315771 r1", "0:149.27 1:149.22", "A:1844296500;C:1523361309;G:1519052310;T:1931907615;N:437866", 149, 149, null, null, 1844296500, 1523361309, 1519052310, 1931907615, 437866, "SRX10895132", "SRS8987959", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.83297, 0.83417, 0.1328, 0.13254, 0.78821, 0.79318, 0.46692, 0.4635, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64337, "SRR14551647", "SRX10895131", "SRS8987955", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "SC 72hpf Sample3", "GSM5315770", null, "tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf", "SC 72hpf Sample3", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf", "GSM5315770", "GSM5315770: SC 72hpf Sample3; Danio rerio; RNA Seq", "GSM5315770", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315770", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "SC72_Sample3_R1_001.fastq.gz SC72_Sample3_R2_001.fastq.gz", "fastq fastq", 5290486005.0, 17724499.0, "GSM5315770 r1", "0:149.26 1:149.22", "A:1416646219;C:1205875601;G:1205458968;T:1462077308;N:427909", 149, 149, null, null, 1416646219, 1205875601, 1205458968, 1462077308, 427909, "SRX10895131", "SRS8987955", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.80356, 0.80484, 0.13757, 0.13551, 0.79017, 0.79569, 0.464, 0.46891, 149, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64338, "SRR14551646", "SRX10895130", "SRS8987954", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "SC 72hpf Sample2", "GSM5315769", null, "tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf", "SC 72hpf Sample2", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf", "GSM5315769", "GSM5315769: SC 72hpf Sample2; Danio rerio; RNA Seq", "GSM5315769", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315769", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "SC72_Sample2_R1_001.fastq.gz SC72_Sample2_R2_001.fastq.gz", "fastq fastq", 5300704321.0, 17740513.0, "GSM5315769 r1", "0:149.42 1:149.37", "A:1270635814;C:1361971808;G:1357145534;T:1310555763;N:395402", 149, 149, null, null, 1270635814, 1361971808, 1357145534, 1310555763, 395402, "SRX10895130", "SRS8987954", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.52849, 0.53398, 0.10216, 0.10317, 0.887, 0.88956, 0.49141, 0.49821, 150, 148, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [64339, "SRR14551645", "SRX10895129", "SRS8987953", "SRP319894", "PRJNA730034", "Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing", "GSE174486", "Transcriptome Analysis", "RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.", null, "pubmed:33975920", null, "SC 72hpf Sample1", "GSM5315768", null, "tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf", "SC 72hpf Sample1", "For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5\u2032 to 3\u2032 and removes bases only at the 3\u2032 end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3\u2032 end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations", "Zebrafish embryo trunk", "72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer\u2019s solution with 2.5mM EDTA and rocked for 15 minutes at 4 \u00b0C. The trunk pieces were washed three times with chilled Dulbecco\u2019s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 \u00b0C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 \u00b0C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 \u03bcm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 \u00b1 750 at each stage were used for RNA sequencing.", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf", "strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf", "GSM5315768", "GSM5315768: SC 72hpf Sample1; Danio rerio; RNA Seq", "GSM5315768", null, "1", "Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing", "GEO Accession:GSM5315768", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP319894", null, "loader:latf load", "SC72_Sample1_R1_001.fastq.gz SC72_Sample1_R2_001.fastq.gz", "fastq fastq", 5239512991.0, 17546095.0, "GSM5315768 r1", "0:149.33 1:149.28", "A:1298269567;C:1306015004;G:1299170862;T:1335241575;N:815983", 149, 149, null, null, 1298269567, 1306015004, 1299170862, 1335241575, 815983, "SRX10895129", "SRS8987953", "SRA1232603", "GEO", "Kucenas Lab, Biology, University of Virginia", 2, 0.61524, 0.62125, 0.10182, 0.10151, 0.87393, 0.87825, 0.47941, 0.47885, 149, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-05-14", "Larval", "Larval", "Trunk", "Surface Structure"], [74790, "SRR24042941", "SRX19844898", "SRS17203996", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 7", "GSM7135698", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 7", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135698", "GSM7135698: mutant epidermis 7; Danio rerio; RNA Seq", "GSM7135698 r1", "GSM7135698", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_7_R1.fq.gz mut_epi_7_R2.fq.gz", "fastq fastq", 5000082600.0, 16666942.0, "GSM7135698 r1", "0:150 1:150", "A:1356614389;C:1145976228;G:1015865485;T:1481123817;N:502681", 150, 150, null, null, 1356614389, 1145976228, 1015865485, 1481123817, 502681, "SRX19844898", "SRS17203996", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.8389, 0.84116, 0.1854, 0.18546, 0.85543, 0.85571, 0.60232, 0.62058, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74791, "SRR24042942", "SRX19844897", "SRS17203995", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 6", "GSM7135697", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 6", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135697", "GSM7135697: mutant epidermis 6; Danio rerio; RNA Seq", "GSM7135697 r1", "GSM7135697", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_6_R1.fq.gz mut_epi_6_R2.fq.gz", "fastq fastq", 5150526900.0, 17168423.0, "GSM7135697 r1", "0:150 1:150", "A:1413867032;C:1148708171;G:1068645696;T:1518782074;N:523927", 150, 150, null, null, 1413867032, 1148708171, 1068645696, 1518782074, 523927, "SRX19844897", "SRS17203995", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.85431, 0.85836, 0.20685, 0.20717, 0.86746, 0.86645, 0.546, 0.5461, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74792, "SRR24042943", "SRX19844896", "SRS17203994", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 5", "GSM7135696", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 5", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135696", "GSM7135696: mutant epidermis 5; Danio rerio; RNA Seq", "GSM7135696 r1", "GSM7135696", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_5_R1.fq.gz mut_epi_5_R2.fq.gz", "fastq fastq", 5444193600.0, 18147312.0, "GSM7135696 r1", "0:150 1:150", "A:1506955248;C:1203830842;G:1100776758;T:1632090095;N:540657", 150, 150, null, null, 1506955248, 1203830842, 1100776758, 1632090095, 540657, "SRX19844896", "SRS17203994", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.84926, 0.85327, 0.24961, 0.24986, 0.86665, 0.8658, 0.59696, 0.59563, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74793, "SRR24042944", "SRX19844895", "SRS17203993", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 4", "GSM7135695", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 4", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135695", "GSM7135695: mutant epidermis 4; Danio rerio; RNA Seq", "GSM7135695 r1", "GSM7135695", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_4_R1.fq.gz mut_epi_4_R2.fq.gz", "fastq fastq", 5002087200.0, 16673624.0, "GSM7135695 r1", "0:150 1:150", "A:1390303577;C:1103953823;G:1001952998;T:1505374747;N:502055", 150, 150, null, null, 1390303577, 1103953823, 1001952998, 1505374747, 502055, "SRX19844895", "SRS17203993", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.84071, 0.84398, 0.25782, 0.25789, 0.89045, 0.89027, 0.594, 0.59396, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74794, "SRR24042945", "SRX19844894", "SRS17203992", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 3", "GSM7135694", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 3", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135694", "GSM7135694: mutant epidermis 3; Danio rerio; RNA Seq", "GSM7135694 r1", "GSM7135694", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_3_R1.fq.gz mut_epi_3_R2.fq.gz", "fastq fastq", 5088778800.0, 16962596.0, "GSM7135694 r1", "0:150 1:150", "A:1423520633;C:1124312893;G:1051927427;T:1488506070;N:511777", 150, 150, null, null, 1423520633, 1124312893, 1051927427, 1488506070, 511777, "SRX19844894", "SRS17203992", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.87032, 0.87262, 0.21802, 0.21697, 0.84478, 0.84516, 0.57085, 0.56848, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74795, "SRR24042946", "SRX19844893", "SRS17203991", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 2", "GSM7135693", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 2", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135693", "GSM7135693: mutant epidermis 2; Danio rerio; RNA Seq", "GSM7135693 r1", "GSM7135693", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_2_R1.fq.gz mut_epi_2_R2.fq.gz", "fastq fastq", 4328463900.0, 14428213.0, "GSM7135693 r1", "0:150 1:150", "A:1188821495;C:969906063;G:882155508;T:1287158594;N:422240", 150, 150, null, null, 1188821495, 969906063, 882155508, 1287158594, 422240, "SRX19844893", "SRS17203991", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.85046, 0.85261, 0.24989, 0.25021, 0.89025, 0.8897, 0.55974, 0.55601, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74796, "SRR24042947", "SRX19844892", "SRS17203990", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "mutant epidermis 1", "GSM7135692", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "mutant epidermis 1", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult", "GSM7135692", "GSM7135692: mutant epidermis 1; Danio rerio; RNA Seq", "GSM7135692 r1", "GSM7135692", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "mut_epi_1_R1.fq.gz mut_epi_1_R2.fq.gz", "fastq fastq", 4852088400.0, 16173628.0, "GSM7135692 r1", "0:150 1:150", "A:1355547120;C:1052947209;G:998601349;T:1444516092;N:476630", 150, 150, null, null, 1355547120, 1052947209, 998601349, 1444516092, 476630, "SRX19844892", "SRS17203990", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.82126, 0.82514, 0.19738, 0.19774, 0.8521, 0.85171, 0.56371, 0.58039, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74797, "SRR24042948", "SRX19844891", "SRS17203989", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 7", "GSM7135691", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 7", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135691", "GSM7135691: sibling epidermis 7; Danio rerio; RNA Seq", "GSM7135691 r1", "GSM7135691", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "sib_epi_7_R1.fq.gz sib_epi_7_R2.fq.gz", "fastq fastq", 5331845400.0, 17772818.0, "GSM7135691 r1", "0:150 1:150", "A:1430690183;C:1254783660;G:1084303117;T:1561520361;N:548079", 150, 150, null, null, 1430690183, 1254783660, 1084303117, 1561520361, 548079, "SRX19844891", "SRS17203989", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.85507, 0.85819, 0.17442, 0.17439, 0.8495, 0.84991, 0.59457, 0.59698, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74798, "SRR24042949", "SRX19844890", "SRS17203987", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 6", "GSM7135690", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 6", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135690", "GSM7135690: sibling epidermis 6; Danio rerio; RNA Seq", "GSM7135690 r1", "GSM7135690", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "sib_epi_6_R1.fq.gz sib_epi_6_R2.fq.gz", "fastq fastq", 5250903600.0, 17503012.0, "GSM7135690 r1", "0:150 1:150", "A:1422246673;C:1203178539;G:1084296067;T:1540644470;N:537851", 150, 150, null, null, 1422246673, 1203178539, 1084296067, 1540644470, 537851, "SRX19844890", "SRS17203987", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.86662, 0.86998, 0.17496, 0.17481, 0.85697, 0.85669, 0.60671, 0.60577, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74799, "SRR24042950", "SRX19844889", "SRS17203988", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 5", "GSM7135689", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 5", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135689", "GSM7135689: sibling epidermis 5; Danio rerio; RNA Seq", "GSM7135689 r1", "GSM7135689", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "sib_epi_5_R1.fq.gz sib_epi_5_R2.fq.gz", "fastq fastq", 5357108100.0, 17857027.0, "GSM7135689 r1", "0:150 1:150", "A:1442683833;C:1246002420;G:1107335060;T:1560544984;N:541803", 150, 150, null, null, 1442683833, 1246002420, 1107335060, 1560544984, 541803, "SRX19844889", "SRS17203988", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.88017, 0.88379, 0.15935, 0.1591, 0.83822, 0.83784, 0.5992, 0.59047, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74800, "SRR24042951", "SRX19844888", "SRS17203986", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 4", "GSM7135688", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 4", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135688", "GSM7135688: sibling epidermis 4; Danio rerio; RNA Seq", "GSM7135688 r1", "GSM7135688", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430475", null, "loader:fastq load.py", "sib_epi_4_R1.fq.gz sib_epi_4_R2.fq.gz", "fastq fastq", 4729031400.0, 15763438.0, "GSM7135688 r1", "0:150 1:150", "A:1269897945;C:1106204392;G:980800578;T:1371651398;N:477087", 150, 150, null, null, 1269897945, 1106204392, 980800578, 1371651398, 477087, "SRX19844888", "SRS17203986", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.89554, 0.89737, 0.15933, 0.1589, 0.84173, 0.84181, 0.57695, 0.58999, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2023-04-02", "Adult", "Adult", "Skin", "Surface Structure"], [74801, "SRR24042952", "SRX19844887", "SRS17203985", "SRP430475", "PRJNA951376", "Spic is required for the differentiation of metaphocyte progenitor cells", "GSE228732", "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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 3", "GSM7135687", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 3", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample", "epidermis", null, "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135687", "GSM7135687: sibling epidermis 3; Danio rerio; RNA Seq", "GSM7135687 r1", "GSM7135687", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. 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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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 2", "GSM7135686", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 2", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. 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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. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings", "parent bioproject:PRJNA951389", "pubmed:37148242", null, "sibling epidermis 1", "GSM7135685", null, "source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "sibling epidermis 1", "Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. 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The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.", null, "tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult", "GSM7135685", "GSM7135685: sibling epidermis 1; Danio rerio; RNA Seq", "GSM7135685 r1", "GSM7135685", "1", "The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria\u2122 IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript\u2122 II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. 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