Total RNA extraction from Rhizobium etli cell or bacteroid pellets - Bertin Instruments

    Microbiology

    Total RNA extraction from Rhizobium etli cell or bacteroid pellets

    Sources: Centre of Microbial and Plant Genetics, Katholieke UniversiteitLeuven, Belgium

    Context

    The laboratory is focused on the study of the genomewide transcriptome of R. etli under diverse conditions. Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In this study, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a wholegenome high-resolution tiling array in the soildwelling a-proteobacterium Rhizobium etli [1].

    [1] Vercruysse et al. BMC Genomics 2010, 11:53http://www.biomedcentral.com/1471-2164/11/53

    Results

    All samples had an RNA Quality Indicator value of 10, using Experion RNA StdSens Chips. The ncRNA peak could be detected in each sample (Figure 1). RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio of all samples were ≥ 2.

    etli cell

    Figure 1: An example of high quality total RNA, illustrating the fragmentation 23S rRNA: (a) small RNA peak including 5S rRNA and the ncRNAs (b) 23S fragment of ~135 bp (c) two 23S fragments of ~1300 bp (d) 16S rRNA (e) intact 23S rRNA.

    Samples were hybridized on a whole-genome tiling array covering the entire R. etli genome sequence (6.5 Mbp in total) and scanned by NimbleGen Systems.
    The Precellys®24 homogenizer is an easy to use device that can be utilized to accomplish a thorough lysis of even stationary phase cells in combination with the lysing kit.

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