{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["74779"], "units": {}, "query_ms": 11.121777992229909}