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These data were produced mainly by the iBeetle consortium [ 72] and a separate publication is in preparation describing the re-annotation of the whole gene set of T. castaneum based on these RNA-Seq data, which can be viewed in a respective genome browser [ 73].
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The preparation of the urine and bile samples were the same as the plasma sample preparation described above.
The preparation, described today in the Proceedings of the National Academy of Sciences, has only been tested so far in animals.
Identification of H. sp. was subsequently based on images from a slide preparation (described in methodology), which were subsequently assessed by Dr. S. Spaulding (Colorado State University) for identification.
Resulting libraries were shipped to the UM/Center for Genome Technology for SOLiD library preparation (described below).
Resulting libraries were quantified via Agilent Bioanalyzer before proceeding to SOLiD platform library preparation (described below).
Then the protocol for cell culture preparation described above was applied.
A second H37Rv strain (TAMU) obtained from ATCC (#27294; preparation described in [15]) was cultured once in Middlebrook 7H9 (M7H9) and frozen for up to 2 3 years before use.
S. aureus α-hemolysin (Sigma-Aldrich, product # H9395) or recombinant α-hemolysin (preparation described above) was added to the cells for 1 hour.
The preparation of the assembly was equal to the preparation described before.
The extraction procedure was same as that for the sample preparation described above.
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