run_metadata: 32803
This data as json
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| 32803 | SRR29453139 | SRX24965354 | SRS21668886 | SRP514613 | PRJNA1125316 | RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE270136 | 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 line. 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 pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were 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. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control. | pubmed:39916610 | kidney derived neutrophils wt Mm infected rep3 | GSM8335404 | source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing | kidney derived neutrophils wt Mm infected rep3 | Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 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 69 118 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 pycardtpu4 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:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum | GSM8335404 | GSM8335404: kidney derived neutrophils wt Mm infected rep3; Danio rerio; RNA Seq | GSM8335404 r1 | GSM8335404 | 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. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP514613 | R16_WT_MM_1.fq.gz R16_WT_MM_2.fq.gz | fastq fastq | 6755682900.0 | 22518943.0 | GSM8335404 r1 | 0:150 1:150 | A:1866248606;C:1494647864;G:1513464764;T:1881229301;N:92365 | 150 | 150 | 1866248606 | 1494647864 | 1513464764 | 1881229301 | 92365 | SRX24965354 | SRS21668886 | SRA1902200 | University of Tampere | University of Tampere | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2024-06-18 | Larval | Larval | Kidney | Renal System |