{"database": "metadata", "table": "run_metadata", "rows": [[59150, "SRR11700447", "SRX8259899", "SRS6601867", "SRP260213", "PRJNA630667", "RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae", "GSE149942", "Transcriptome Analysis", "The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer\u00ae Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.", null, "pubmed:33852860", null, "cxcr3.2mu rep3", "GSM4518497", null, "tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ", "cxcr3.2mu rep3", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample", "FACS mpeg1: mCherryF positive cells", null, "3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers\u2019 instructions. cDNA synthesis and amplification was done using the SMARTer\u00ae Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer\u2019s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.", null, "age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ", "GSM4518497", "GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq", "GSM4518497", null, "1", "3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer\u00ae Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.", "GEO Accession:GSM4518497", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP260213", null, null, "mu3_1.fastq.gz", "fastq", 425713881.0, 8347331.0, "GSM4518497 r1", "0:51", "A:122037955;C:83276458;G:83884392;T:136385789;N:129287", 51, null, null, null, 122037955, 83276458, 83884392, 136385789, 129287, "SRX8259899", "SRS6601867", "SRA1072497", "GEO", "LSHTM", 1, 0.79761, null, 0.24807, null, 0.78031, null, 0.55233, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-06", "Larval", "Larval", "Blood", "Hematopoietic 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": ["59150"], "units": {}, "query_ms": 7.258616999024525}