{"database": "metadata", "table": "run_metadata", "rows": [[28392, "SRR26213388", "SRX21923916", "SRS19008427", "SRP463773", "PRJNA1022165", "Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.", "GSE244308", "Transcriptome Analysis", "Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.", null, null, null, "Neutrophils  WT  infected 1", "GSM7813282", null, "tissue:Neutrophil|developmental stage:larvae|cell type:Neutrophil|genotype:Tglyz:DsRED2/WT|infection:Salm1lla typhimurium|geo loc name:missing|collection date:missing", "Neutrophils  WT  infected 1", "The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM  Log2FC  and adj P value of DEGs comparing Per2Infected and WTInfected samples.", "Neutrophil", "At 52 hpf 4 hours post lights on  Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 /  zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.", "Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.", "Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions", "developmental stage:larvae|cell type:Neutrophil|genotype:Tglyz:DsRED2/WT|infection:Salm1lla typhimurium", "GSM7813282", "GSM7813282: Neutrophils  WT  infected 1; Danio rerio; RNA Seq", "GSM7813282 r1", "GSM7813282", "1", "Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP463773", null, "loader:fastq load.py", "WTInfected-1_S5_R1_001.fastq.gz", "fastq", 2629109363.0, 34890907.0, "GSM7813282 r1", "0:75.35", "A:717313087;C:596048245;G:613729475;T:701790568;N:227988", 75, null, null, null, 717313087, 596048245, 613729475, 701790568, 227988, "SRX21923916", "SRS19008427", "SRA1722831", "The University of Auckland", "The University of Auckland", 1, 0.88964, null, 0.13171, null, 0.81142, null, 0.49273, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "New Zealand", "2023-09-28", "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": ["28392"], "units": {}, "query_ms": 11.175525999988167}