{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"smartseq\" and tissue_curation_coarse = \"Respiratory System\"", "rows": [[60514, "SRR12340121", "SRX8839908", "SRS7103142", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 3", "GSM4698505", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 3", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698505", "GSM4698505: sox17 gill DsRedx 3; Danio rerio; RNA Seq", "GSM4698505", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698505", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_3_R1.fq.gz sox17_gill_DsRedx_3_R2.fq.gz", "fastq fastq", 6482204823.0, 22206962.0, "GSM4698505 r1", "0:146.24 1:145.66", "A:1892664132;C:1333446985;G:1270670352;T:1985394285;N:29069", 146, 145, null, null, 1892664132, 1333446985, 1270670352, 1985394285, 29069, "SRX8839908", "SRS7103142", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.79891, 0.79555, 0.23795, 0.23516, 0.886, 0.88613, 0.48969, 0.48724, 150, 148, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60515, "SRR12340120", "SRX8839907", "SRS7103140", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 2", "GSM4698504", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 2", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698504", "GSM4698504: sox17 gill DsRedx 2; Danio rerio; RNA Seq", "GSM4698504", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698504", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_2_R1.fq.gz sox17_gill_DsRedx_2_R2.fq.gz", "fastq fastq", 6871522969.0, 23718551.0, "GSM4698504 r1", "0:145.07 1:144.64", "A:1996597634;C:1433447769;G:1330303568;T:2111142421;N:31577", 145, 144, null, null, 1996597634, 1433447769, 1330303568, 2111142421, 31577, "SRX8839907", "SRS7103140", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.77789, 0.77647, 0.23871, 0.23784, 0.90319, 0.90402, 0.59462, 0.59357, 149, 80, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60516, "SRR12340119", "SRX8839906", "SRS7103139", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 1", "GSM4698503", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 1", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698503", "GSM4698503: sox17 gill DsRedx 1; Danio rerio; RNA Seq", "GSM4698503", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698503", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_1_R1.fq.gz sox17_gill_DsRedx_1_R2.fq.gz", "fastq fastq", 6640801871.0, 23132663.0, "GSM4698503 r1", "0:143.42 1:143.65", "A:1787496811;C:1555982056;G:1401318306;T:1895972742;N:31956", 143, 143, null, null, 1787496811, 1555982056, 1401318306, 1895972742, 31956, "SRX8839906", "SRS7103139", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82205, 0.82023, 0.17657, 0.17516, 0.88799, 0.88846, 0.60101, 0.5999, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60517, "SRR12340118", "SRX8839905", "SRS7103141", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 3", "GSM4698502", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 3", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698502", "GSM4698502: sox17 gill GFP 3; Danio rerio; RNA Seq", "GSM4698502", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698502", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_3_R1.fq.gz sox17_gill_GFP_3_R2.fq.gz", "fastq fastq", 5881408853.0, 20262087.0, "GSM4698502 r1", "0:145.09 1:145.18", "A:1611164278;C:1359776238;G:1263385328;T:1647055163;N:27846", 145, 145, null, null, 1611164278, 1359776238, 1263385328, 1647055163, 27846, "SRX8839905", "SRS7103141", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.85631, 0.85552, 0.14127, 0.14135, 0.88972, 0.89065, 0.53836, 0.53645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60518, "SRR12340117", "SRX8839904", "SRS7103138", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 2", "GSM4698501", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 2", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698501", "GSM4698501: sox17 gill GFP 2; Danio rerio; RNA Seq", "GSM4698501", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698501", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_2_R1.fq.gz sox17_gill_GFP_2_R2.fq.gz", "fastq fastq", 6629269698.0, 23040040.0, "GSM4698501 r1", "0:143.67 1:144.06", "A:1792321281;C:1562626172;G:1410652523;T:1863639213;N:30509", 143, 144, null, null, 1792321281, 1562626172, 1410652523, 1863639213, 30509, "SRX8839904", "SRS7103138", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.87337, 0.87168, 0.16298, 0.16158, 0.86563, 0.86582, 0.57739, 0.58009, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60519, "SRR12340116", "SRX8839903", "SRS7103137", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine  we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP  sox17 gill DsRedx and intestine sox17 intestine GFP  sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine  including GFP labelled metaphocytes and DsRedx labelled macrophages  were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 1", "GSM4698500", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 1", "Raw reads were first aligned to zebrafish reference genome danRer11\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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698500", "GSM4698500: sox17 gill GFP 1; Danio rerio; RNA Seq", "GSM4698500", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698500", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_1_R1.fq.gz sox17_gill_GFP_1_R2.fq.gz", "fastq fastq", 8550712115.0, 29745129.0, "GSM4698500 r1", "0:143.49 1:143.98", "A:2279816799;C:2045513877;G:1883280335;T:2342060508;N:40596", 143, 143, null, null, 2279816799, 2045513877, 1883280335, 2342060508, 40596, "SRX8839903", "SRS7103137", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.87481, 0.87331, 0.14783, 0.14775, 0.84824, 0.84946, 0.54943, 0.47083, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [74777, "SRR24042928", "SRX19844911", "SRS17204009", "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 gill 8", "GSM7135711", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 8", "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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135711", "GSM7135711: mutant gill 8; Danio rerio; RNA Seq", "GSM7135711 r1", "GSM7135711", "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_gill_8_R1.fq.gz mut_gill_8_R2.fq.gz", "fastq fastq", 4676495100.0, 15588317.0, "GSM7135711 r1", "0:150 1:150", "A:1307407255;C:1023522602;G:969790674;T:1375306960;N:467609", 150, 150, null, null, 1307407255, 1023522602, 969790674, 1375306960, 467609, "SRX19844911", "SRS17204009", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.83959, 0.8448, 0.26782, 0.26778, 0.87125, 0.87144, 0.56023, 0.56037, 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", "Gill", "Respiratory System"], [74778, "SRR24042929", "SRX19844910", "SRS17204008", "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 gill 7", "GSM7135710", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135710", "GSM7135710: mutant gill 7; Danio rerio; RNA Seq", "GSM7135710 r1", "GSM7135710", "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_gill_7_R1.fq.gz mut_gill_7_R2.fq.gz", "fastq fastq", 5888494500.0, 19628315.0, "GSM7135710 r1", "0:150 1:150", "A:1618640164;C:1326869398;G:1198422598;T:1743959857;N:602483", 150, 150, null, null, 1618640164, 1326869398, 1198422598, 1743959857, 602483, "SRX19844910", "SRS17204008", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.84262, 0.84414, 0.2211, 0.2217, 0.85208, 0.85275, 0.54003, 0.5392, 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", "Gill", "Respiratory System"], [74779, "SRR24042930", "SRX19844909", "SRS17204007", "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 gill 6", "GSM7135709", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135709", "GSM7135709: mutant gill 6; Danio rerio; RNA Seq", "GSM7135709 r1", "GSM7135709", "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_gill_6_R1.fq.gz mut_gill_6_R2.fq.gz", "fastq fastq", 5319891900.0, 17732973.0, "GSM7135709 r1", "0:150 1:150", "A:1487641547;C:1157753055;G:1092549232;T:1581414608;N:533458", 150, 150, null, null, 1487641547, 1157753055, 1092549232, 1581414608, 533458, "SRX19844909", "SRS17204007", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.84896, 0.85199, 0.24621, 0.24605, 0.83378, 0.83337, 0.55455, 0.55559, 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", "Gill", "Respiratory System"], [74780, "SRR24042931", "SRX19844908", "SRS17204006", "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 gill 5", "GSM7135708", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135708", "GSM7135708: mutant gill 5; Danio rerio; RNA Seq", "GSM7135708 r1", "GSM7135708", "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_gill_5_R1.fq.gz mut_gill_5_R2.fq.gz", "fastq fastq", 5529933300.0, 18433111.0, "GSM7135708 r1", "0:150 1:150", "A:1544115928;C:1211935586;G:1126417556;T:1646909383;N:554847", 150, 150, null, null, 1544115928, 1211935586, 1126417556, 1646909383, 554847, "SRX19844908", "SRS17204006", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.85153, 0.85305, 0.23595, 0.23538, 0.83463, 0.83522, 0.55289, 0.5526, 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", "Gill", "Respiratory System"], [74781, "SRR24042932", "SRX19844907", "SRS17204005", "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 gill 4", "GSM7135707", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135707", "GSM7135707: mutant gill 4; Danio rerio; RNA Seq", "GSM7135707 r1", "GSM7135707", "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_gill_4_R1.fq.gz mut_gill_4_R2.fq.gz", "fastq fastq", 5181547800.0, 17271826.0, "GSM7135707 r1", "0:150 1:150", "A:1461607714;C:1119875397;G:1036275299;T:1563269275;N:520115", 150, 150, null, null, 1461607714, 1119875397, 1036275299, 1563269275, 520115, "SRX19844907", "SRS17204005", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.82652, 0.82859, 0.2619, 0.26087, 0.8508, 0.851, 0.5174, 0.51758, 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", "Gill", "Respiratory System"], [74782, "SRR24042933", "SRX19844906", "SRS17204004", "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 gill 3", "GSM7135706", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135706", "GSM7135706: mutant gill 3; Danio rerio; RNA Seq", "GSM7135706 r1", "GSM7135706", "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_gill_3_R1.fq.gz mut_gill_3_R2.fq.gz", "fastq fastq", 5914269900.0, 19714233.0, "GSM7135706 r1", "0:150 1:150", "A:1744887146;C:1199785696;G:1139441688;T:1829560268;N:595102", 150, 150, null, null, 1744887146, 1199785696, 1139441688, 1829560268, 595102, "SRX19844906", "SRS17204004", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.81829, 0.82058, 0.35062, 0.34936, 0.82822, 0.82818, 0.45594, 0.45957, 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", "Gill", "Respiratory System"], [74783, "SRR24042934", "SRX19844905", "SRS17204003", "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 gill 2", "GSM7135705", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135705", "GSM7135705: mutant gill 2; Danio rerio; RNA Seq", "GSM7135705 r1", "GSM7135705", "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_gill_2_R1.fq.gz mut_gill_2_R2.fq.gz", "fastq fastq", 4408680900.0, 14695603.0, "GSM7135705 r1", "0:150 1:150", "A:1244600117;C:952046549;G:896094438;T:1315516801;N:422995", 150, 150, null, null, 1244600117, 952046549, 896094438, 1315516801, 422995, "SRX19844905", "SRS17204003", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.84142, 0.84219, 0.24006, 0.23884, 0.84072, 0.84017, 0.54492, 0.53976, 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", "Gill", "Respiratory System"], [74784, "SRR24042935", "SRX19844904", "SRS17204002", "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 gill 1", "GSM7135704", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "mutant gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult", "GSM7135704", "GSM7135704: mutant gill 1; Danio rerio; RNA Seq", "GSM7135704 r1", "GSM7135704", "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_gill_1_R1.fq.gz mut_gill_1_R2.fq.gz", "fastq fastq", 5737020900.0, 19123403.0, "GSM7135704 r1", "0:150 1:150", "A:1628971228;C:1225892373;G:1171419964;T:1710176758;N:560577", 150, 150, null, null, 1628971228, 1225892373, 1171419964, 1710176758, 560577, "SRX19844904", "SRS17204002", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.85749, 0.85886, 0.22848, 0.22786, 0.84751, 0.8478, 0.54349, 0.54831, 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", "Gill", "Respiratory System"], [74785, "SRR24042936", "SRX19844903", "SRS17204001", "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 gill 5", "GSM7135703", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "sibling gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "GSM7135703", "GSM7135703: sibling gill 5; Danio rerio; RNA Seq", "GSM7135703 r1", "GSM7135703", "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_gill_5_R1.fq.gz sib_gill_5_R2.fq.gz", "fastq fastq", 6562140600.0, 21873802.0, "GSM7135703 r1", "0:150 1:150", "A:1779900685;C:1529690989;G:1371763678;T:1880116831;N:668417", 150, 150, null, null, 1779900685, 1529690989, 1371763678, 1880116831, 668417, "SRX19844903", "SRS17204001", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.88218, 0.88445, 0.15726, 0.15686, 0.80844, 0.80856, 0.477, 0.47442, 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", "Gill", "Respiratory System"], [74786, "SRR24042937", "SRX19844902", "SRS17204000", "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 gill 4", "GSM7135702", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "sibling gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "GSM7135702", "GSM7135702: sibling gill 4; Danio rerio; RNA Seq", "GSM7135702 r1", "GSM7135702", "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_gill_4_R1.fq.gz sib_gill_4_R2.fq.gz", "fastq fastq", 6257889900.0, 20859633.0, "GSM7135702 r1", "0:150 1:150", "A:1662270061;C:1479033481;G:1292962058;T:1822988793;N:635507", 150, 150, null, null, 1662270061, 1479033481, 1292962058, 1822988793, 635507, "SRX19844902", "SRS17204000", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.87917, 0.88287, 0.17274, 0.173, 0.83287, 0.8325, 0.54714, 0.55034, 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", "Gill", "Respiratory System"], [74787, "SRR24042938", "SRX19844901", "SRS17203999", "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 gill 3", "GSM7135701", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "sibling gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "GSM7135701", "GSM7135701: sibling gill 3; Danio rerio; RNA Seq", "GSM7135701 r1", "GSM7135701", "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_gill_3_R1.fq.gz sib_gill_3_R2.fq.gz", "fastq fastq", 4697288100.0, 15657627.0, "GSM7135701 r1", "0:150 1:150", "A:1267251861;C:1084859605;G:951792210;T:1393022956;N:361468", 150, 150, null, null, 1267251861, 1084859605, 951792210, 1393022956, 361468, "SRX19844901", "SRS17203999", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.87119, 0.87101, 0.22114, 0.22034, 0.84822, 0.84638, 0.56814, 0.56703, 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", "Gill", "Respiratory System"], [74788, "SRR24042939", "SRX19844900", "SRS17203998", "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 gill 2", "GSM7135700", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "sibling gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "GSM7135700", "GSM7135700: sibling gill 2; Danio rerio; RNA Seq", "GSM7135700 r1", "GSM7135700", "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_gill_2_R1.fq.gz sib_gill_2_R2.fq.gz", "fastq fastq", 4409361900.0, 14697873.0, "GSM7135700 r1", "0:150 1:150", "A:1190780563;C:1018286434;G:902403781;T:1297459939;N:431183", 150, 150, null, null, 1190780563, 1018286434, 902403781, 1297459939, 431183, "SRX19844900", "SRS17203998", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.88022, 0.88304, 0.17039, 0.17149, 0.82793, 0.82856, 0.55968, 0.56548, 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", "Gill", "Respiratory System"], [74789, "SRR24042940", "SRX19844899", "SRS17203997", "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 gill 1", "GSM7135699", null, "source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "sibling gill 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", "gill", 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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult", "GSM7135699", "GSM7135699: sibling gill 1; Danio rerio; RNA Seq", "GSM7135699 r1", "GSM7135699", "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_gill_1_R1.fq.gz sib_gill_1_R2.fq.gz", "fastq fastq", 6054959100.0, 20183197.0, "GSM7135699 r1", "0:150 1:150", "A:1655928049;C:1376589574;G:1251684181;T:1770148028;N:609268", 150, 150, null, null, 1655928049, 1376589574, 1251684181, 1770148028, 609268, "SRX19844899", "SRS17203997", "SRA1614434", "WEN lab, Life Science, Hong Kong University of Science and Technology", "WEN lab, Life Science, Hong Kong University of Science and Technology", 2, 0.88342, 0.88635, 0.14131, 0.14119, 0.83349, 0.83343, 0.57723, 0.59252, 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", "Gill", "Respiratory System"]], 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"tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], 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