Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Mycobacterium tuberculosis TraSH experiment: Growth in wild type C57BL/6J versus iNOS-/- mice

ABSTRACT: A M. tuberculosis transposon library was used to infect WT and iNOS-/- mice. Surviving mutants were recovered from spleens, genomic DNA was extracted, and labeled probes were synthesized from transposon ends. Probes from each WT mouse were hybridized with probes from a similar iNOS-/- mouse. Two-condition experiment, Growth in WT vs. iNOS-/- mice. Biological replicates: TraSH probe made from 5 wild type and 5 iNOS-/- mice after 3 weeks of infection and from 8 wild type and 8 iNOS-/- mice after 4 weeks of infection. Technical replicates: TraSH probe was synthesized twice from each mouse and dyes were swapped. One array contains probe from one iNOS-/- and one WT mouse. Each biological replicate has two arrays, representing technical replicate dye swaps from one iNOS-/- and one WT mouse.

ORGANISM(S): Mycobacterium tuberculosis

SUBMITTER: Christopher Sassetti

PROVIDER: E-GEOD-17706 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Phthiocerol dimycocerosate transport is required for resisting interferon-gamma-independent immunity.

Murry Jeffrey P JP Pandey Amit K AK Sassetti Christopher M CM Rubin Eric J EJ

The Journal of infectious diseases 20090901 5

Nitric oxide (NO), which is an important component of immunity to Mycobacterium tuberculosis, has both cytotoxic and immune regulatory functions. We examined the way that this molecule interacts with M. tuberculosis in vivo by screening for bacterial mutations that alter growth in mice that are unable to produce inducible NO synthase (iNOS), the dominant source of NO during infection. We found that very few bacterial genes appeared to be specifically required for resistance to NO in vivo. Instea ...[more]

PMID: 19622047

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Project description:Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNA from poly A-containing RNA obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 (99%) of the arrayed PBCV-1 CDSs are expressed at some time in the virus life cycle in the laboratory; iii) 227 (62%) of the CDSs are expressed before virus DNA synthesis begins; iv) these 227 CDSs were grouped into two classes: 127 transcripts disappear prior to initiation of virus DNA synthesis (considered early) and 100 transcripts are still detected after virus DNA synthesis begins (considered early/late); v) 133 (36%) of the CDSs are expressed after virus DNA synthesis begins (considered late); vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor aphidicolin prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 lifecycle. Time course analysis of chlorella virus PBCV-1: cDNAs from poly A-containing RNAs isolated from cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against a reference sample on the microarrays. Three independent biological replica, four technical replica of the genome per array. Time course analysis of chlorella virus PBCV-1 gene expression in the presence of aphidicolin: cDNAs from poly A-containing RNAs isolated from aphidicolin-treated cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against non-treated, infected samples from the same time points. Three independent biological replica, four technical replica of the genome per array.

Dataset Information

Mycobacterium tuberculosis TraSH experiment: Growth in wild type C57BL/6J versus iNOS-/- mice

Publications

Phthiocerol dimycocerosate transport is required for resisting interferon-gamma-independent immunity.

Similar Datasets

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