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| Status |
Public on Aug 01, 2013 |
| Title |
Strand-specific RNA-seq analysis of three streptomycetes |
| Organisms |
Streptomyces coelicolor; Streptomyces avermitilis; Streptomyces venezuelae |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters.
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| Overall design |
For each of the three species (S. coelicolor, S. avermitilis, S. venezuelae) two libraries were created. The first was a long-read library, where total RNA was depleted of rRNA. The second was a short read library, where total RNA was size selected (40-300 nucleotides) prior to library creation. The long-read library allowed the profiling of mRNAs and asRNAs, while the short-read library was enriched for small RNAs (sRNAs).
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| Contributor(s) |
Elliot MA, Moody MJ, Young RA, Jones SE |
| Citation(s) |
23947565 |
| |
| Submission date |
Apr 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew John Moody |
| E-mail(s) |
[email protected]
|
| Organization name |
McMaster University
|
| Department |
Biology
|
| Street address |
Life Sciences Building Rm 323, McMaster University, 1280 Main St W
|
| City |
Hamilton |
| State/province |
ON |
| ZIP/Postal code |
L8S4L8 |
| Country |
Canada |
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| Platforms (3) |
| GPL17012 |
Illumina HiSeq 2000 (Streptomyces coelicolor) |
| GPL17013 |
Illumina HiSeq 2000 (Streptomyces avermitilis) |
| GPL17014 |
Illumina HiSeq 2000 (Streptomyces venezuelae) |
|
| Samples (6)
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| Relations |
| BioProject |
PRJNA196870 |
| SRA |
SRP021022 |
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