{"database": "metadata", "table": "run_metadata", "rows": [[49087, "SRR7664345", "SRX4524952", "SRS3643046", "SRP156914", "PRJNA485334", "Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463]", "GSE118350", "Transcriptome Analysis", "Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. In addition  we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen  we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line  the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed  four biological replicates in each group.", null, "pubmed:31626817", null, "mutant463 inf rep4", "GSM3325717", null, "tissue:zebrafish kidney|strain:mutant463", "mutant463 inf rep4", "Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts\u00a0 Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample.", "zebrafish kidney", "5 mpf to 6 mpf zebrafish were infected with 5   9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection.", "Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID:\u00a074104 according to the manufacturer\u2019s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols.", "The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct.", "strain:mutant463", "GSM3325717", "GSM3325717: mutant463 inf rep4; Danio rerio; RNA Seq", "GSM3325717", null, "1", "Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID:\u00a074104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM3325717", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP156914", null, null, "F1_463_4_1.fq.gz F1_463_4_2.fq.gz", "fastq fastq", 7892745600.0, 26309152.0, "GSM3325717 r1", "0:150 1:150", "A:2102605709;C:1854325558;G:1849161474;T:2085489415;N:1163444", 150, 150, null, null, 2102605709, 1854325558, 1849161474, 2085489415, 1163444, "SRX4524952", "SRS3643046", "SRA756218", "GEO", "University of Tampere", 2, 0.9279, 0.91721, 0.05059, 0.0497, 0.7302, 0.73448, 0.51354, 0.51569, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2018-08-09", "Multi-stage", "Multi-stage", "Kidney", "Renal 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": ["49087"], "units": {}, "query_ms": 8.52198300708551}