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| Status |
Public on Jan 05, 2016 |
| Title |
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus |
| Organism |
Staphylococcus aureus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions.
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| Overall design |
Four RNAseq data sets in total. Each sample was generated by pooling three independent biological replicate RNA preps
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| Contributor(s) |
Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN |
| Citation(s) |
26861020 |
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| Submission date |
Nov 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronan Kevin Carroll |
| E-mail(s) |
carrolr3@ohio.edu
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| Phone |
740-593-2201
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| Organization name |
Ohio University
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| Department |
Biological Sciences
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| Street address |
107 Irvine Hall
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| City |
Athens |
| State/province |
OHIO |
| ZIP/Postal code |
45701 |
| Country |
USA |
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| Platforms (1) |
| GPL19476 |
Ion Torrent PGM (Staphylococcus aureus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA301968 |
| SRA |
SRP066096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74936_RAW.tar |
600.0 Kb |
(http)(custom) |
TAR (of XLS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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