{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"smartseq\" and tissue_curation = \"Skin\"", "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. 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: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. 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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"], [51261, "SRR8632324", "SRX5431025", "SRS4411020", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "Krt4+", "GSM3629719", null, "source name:keratinocytes|strain background:AB|gentoype/variation:wild type|tissue:keratinocytes", "Krt4+", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: \u201c alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000\u201d for Samples 6 11: \u201c outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: \u201c s 1 \u2013Q 10\u201d for Samples 6 11 \" p Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "keratinocytes", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:wild type|tissue:keratinocytes", "GSM3629719", "GSM3629719: Krt4+; Danio rerio; RNA Seq", "GSM3629719", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..", "GEO Accession:GSM3629719", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186864", null, null, "krt4.fastq.gz", "fastq", 101078150.0, 2021563.0, "GSM3629719 r1", "0:50", "A:18002613;C:22778088;G:30701792;T:29589610;N:6047", 50, null, null, null, 18002613, 22778088, 30701792, 29589610, 6047, "SRX5431025", "SRS4411020", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 1, 0.05911, null, 0.00807, null, 0.97461, null, 0.77586, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Skin", "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. 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