run_metadata: 29698
This data as json
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| 29698 | SRR27406967 | SRX23082008 | SRS20040776 | SRP481061 | PRJNA1060611 | The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae | GSE252417 | Transcriptome Analysis | Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0 1 2 3 4 5 6 8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0 3 4 5 6 and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf which was in duplo. | M 8 1 [IL 13 30 19] | GSM8001092 | source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing | M 8 1 [IL 13 30 19] | GeneTiles Veneman et al. 2015; Immunogenetics 67 135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene; Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name "raw" and "scaled" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or CTRL/MEAS scaled; p value; adjusted p value; best exon p value | whole embryo/larva | 16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone. | Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2. | AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius. | strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva | GSM8001092 | GSM8001092: M 8 1 [IL 13 30 19]; Danio rerio; RNA Seq | GSM8001092 r1 | GSM8001092 | 1 | Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP481061 | IL-13-30-19_TAGCTT_L002_R1_001.fastq.gz | fastq | 62964855.0 | 1234605.0 | GSM8001092 r1 | 0:51 | A:15317447;C:16365148;G:15892573;T:15339413;N:50274 | 51 | 15317447 | 16365148 | 15892573 | 15339413 | 50274 | SRX23082008 | SRS20040776 | SRA1779138 | Future Genomics Technologies BV | Future Genomics Technologies BV | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Netherlands | 2024-01-03 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |