PMID:23899370
| Citation |
Li, S, Dong, X and Su, Z (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 14:520 |
|---|---|
| Abstract |
Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. |
| Links |
PubMed PMC3734233 Online version:10.1186/1471-2164-14-520 |
| Keywords |
Algorithms; Escherichia coli/genetics; Genes, Bacterial; RNA, Messenger/genetics; Sequence Analysis, RNA; Transcriptome |
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Data
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| Strain/Organism | Assay | Analyte | Variable Conditions | Notes | Links |
|---|---|---|---|---|---|
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MG1655 |
RNA-seq |
total RNA |
Heat shock |
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MG1655 |
RNA-seq |
total RNA |
phosphorus starvation |
| |
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</protect>
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