{"database": "metadata", "table": "run_metadata", "rows": [[34540, "SRR32064722", "SRX27413525", "SRS23843184", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep1", "GSM8748658", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep1", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 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 ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748658", "GSM8748658: kidney derived neutrophils  homozygous  Mm infected  rep1; Danio rerio; RNA Seq", "GSM8748658 r1", "GSM8748658", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA14_H_MM_R_1.fq.gz RNA14_H_MM_R_2.fq.gz", "fastq fastq", 6516002400.0, 21720008.0, "GSM8748658 r1", "0:150 1:150", "A:1798422932;C:1471942244;G:1470322290;T:1774672386;N:642548", 150, 150, null, null, 1798422932, 1471942244, 1470322290, 1774672386, 642548, "SRX27413525", "SRS23843184", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "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": ["34540"], "units": {}, "query_ms": 8.356227001058869}