run_metadata: 49085
This data as json
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| 49085 | SRR7659028 | SRX4520645 | SRS3639021 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | 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. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | AB 2: WT inf rep2 | GSM3324246 | source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | AB 2: WT inf rep2 | 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 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. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 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. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | GSM3324246 | GSM3324246: AB 2: WT inf rep2; Danio rerio; RNA Seq | GSM3324246 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 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:GSM3324246 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | AB_2_2.fq.gz AB_2_1.fq.gz | fastq fastq | 7060829400.0 | 23536098.0 | GSM3324246 r1 | 0:150 1:150 | A:1875609739;C:1663056551;G:1660410877;T:1861028532;N:723701 | 150 | 150 | 1875609739 | 1663056551 | 1660410877 | 1861028532 | 723701 | SRX4520645 | SRS3639021 | SRA755536 | GEO | University of Tampere | 2 | 0.92483 | 0.9177 | 0.04614 | 0.04584 | 0.73012 | 0.73389 | 0.52324 | 0.52808 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System |