Research article
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
- † Equal contributors
1 Department of Food Science, Cornell University, Ithaca, NY, USA
2 Computational Biology Service Unit, Cornell University, Ithaca, NY, USA
3 Department of Computer Science, Cornell University, Ithaca, NY, USA
4 School of Mathematics and Statistics, University of Sydney, NSW, Australia
5 Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY, USA
6 United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
7 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
BMC Genomics 2009, 10:641 doi:10.1186/1471-2164-10-641
Published: 30 December 2009Additional files
Additional file 1:
Sequencibility text file. The resulting plot, when used in conjunction with the Artemis genome browser, shows the regions that can (0) and cannot (1) be sequenced in the 10403S pseudochromosome with the Illumina Genome Analyzer. Regions that cannot be sequenced appear as high peaks.
Format: TXT Size: 8.2MB Download file
Additional file 2:
RNA-Seq average GEI and TaqMan qRT-PCR absolute copy number of select genes.
Format: XLS Size: 26KB Download file
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Additional file 3:
Cumulative frequency of average GEI in L. monocytogenes 10403S. The vertical line indicates an average GEI of 0.7 reads, which is the cut-off used to identify transcription. The graph shows that about 83% of the genes fall at the right of the average GEI cut-off of 0.7 reads and were therefore considered transcribed.
Format: TIFF Size: 365KB Download file
Additional file 4:
Access database. All RNA-Seq data are provided in an Access database file. This database contains information on the annotated CDS and ncRNAs with their 10403S locus name, 10403S start and end coordinates, lengths, strand, EGD-e locus, EGD-e gene name, EGD-e common name, EGD-e role category, codon bias, GEI, average GEI in 10403S and ΔsigB strains, fold change for the four possible comparisons involving the two replicates with 10403S and the ΔsigB strains, q-values of the binomial tests, operon annotation, promoter annotation, list of σB-dependent genes identified in this study, and data from the other 3 studies of the σB regulon in L. monocytogenes using microarrays including Ollinger et al. [12], Hain et al. [11], and Raengpradub et al. [10].
Format: MDB Size: 3.6MB Download file
Additional file 5:
ncRNAs identified by RNA-Seq.
Format: XLS Size: 44KB Download file
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Additional file 6:
ncRNAs previously described in L. monocytogenes strain EGD-e but not identified in this study.
Format: XLS Size: 36KB Download file
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Additional file 7:
Genes up-regulated by σB.
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Additional file 8:
Comparison of genes found to be σB-dependent by microarray analysis and not by RNA-Seq.
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Additional file 9:
Distribution of quality scores for all RNA-Seq runs. The quality of the RNA-Seq reads was analyzed using the correspondence between the quality score and error probability; these analyses were performed on Illumina RNA-Seq quality scores that were converted to phred format http://www.phrap.com/phred/ webcite.
Format: TIFF Size: 3.4MB Download file
Additional file 10:
Genbank (gbk) file with ncRNAs identified here.
Format: GBK Size: 4MB Download file
Additional file 11:
Coefficient of variation among RNA-Seq replicates by strain. (A) Histogram of the coefficient of variation (standard deviation/mean) for genes with GEI > 0 in both replicates for 10403S and ΔsigB strain. There is less variation between ΔsigB replicates compared to the 10403S replicates, but very few genes have a coefficient > 0.6. (B) Histogram depicting the GEI of one replicate for genes where the other replicate GEI = 0. The replicate GEI of the gene for which the other replicate is 0 (zero) is typically very low (GEI < 0.7).
Format: TIFF Size: 516KB Download file
Additional file 12:
Coverage file with the normalized RNA-Seq coverage for the 4 RNA-Seq runs.
Format: ZIP Size: 2.5MB Download file
Additional file 13:
σB-dependent promoters used for HMM search.
Format: XLS Size: 26KB Download file
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