Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain and Growth Conditions
2.2. RNA Sequencing
2.3. Principal Component Analysis
2.4. Regulon and Gene Ontology Enrichments
2.5. TER Estimation
3. Results
3.1. General Properties of the Dataset
3.1.1. Differentially Expressed Genes
3.1.2. Principal Component Analysis
3.1.3. Regulon and Gene Ontology Enrichments
3.2. Transcriptional Elongation Rates
3.2.1. Correlation Analyses of TERs and Delay Times
4. Discussion
4.1. Gene Expression Patterns
4.1.1. Iron Balance
4.1.2. Expression of Oxidases
4.2. Transcriptional Elongation Rates
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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ρ of TER | p Value | ρ of Delay Time | p Value | |
---|---|---|---|---|
upregulation | −0.084 | 0.43 | 0.37 | 2.7 × 10−4 |
maximal FC | −0.17 | 0.10 | 0.416 | 7.2 × 10−6 |
maximal RPKM | −0.10 | 0.36 | 0.05 | 0.61 |
GC content | −0.11 | 0.32 | −0.04 | 0.73 |
CAI | −0.23 | 0.03 | −0.10 | 0.35 |
ITE | −0.25 | 0.02 | −0.15 | 0.14 |
RNA folding energy | 0.17 | 0.10 | 0.12 | 0.25 |
regulated by Cra * | −0.03 | 0.75 | −0.29 | 0.01 |
regulated by FNR * | −0.13 | 0.21 | −0.21 | 0.04 |
regulated by Fur-Fe * | −0.12 | 0.28 | 0.22 | 0.04 |
controlled by sigma S | −0.15 | 0.15 | −0.22 | 0.04 |
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Von Wulffen, J.; Ulmer, A.; Jäger, G.; Sawodny, O.; Feuer, R. Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. Genes 2017, 8, 90. https://doi.org/10.3390/genes8030090
Von Wulffen J, Ulmer A, Jäger G, Sawodny O, Feuer R. Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. Genes. 2017; 8(3):90. https://doi.org/10.3390/genes8030090
Chicago/Turabian StyleVon Wulffen, Joachim, Andreas Ulmer, Günter Jäger, Oliver Sawodny, and Ronny Feuer. 2017. "Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics" Genes 8, no. 3: 90. https://doi.org/10.3390/genes8030090