Research
Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus
1 Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
2 University of Freiburg, Faculty of Biology, D-79104 Freiburg, Germany
3 Technion - Israel Institute of Technology, Faculty of Biology, Haifa 32000, Israel
4 University of Algarve, Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine, 8005-139 Faro, Portugal
5 Humboldt University, Institute for Theoretical Biology, Charité, 10115 Berlin, Germany
6 Harvard Medical School, Department of Genetics, Biopolymers Facility, Boston, MA 02115, USA
7 PerkinElmer Life and Analytical Sciences, Waltham, MA 02451, USA
Genome Biology 2010, 11:R54 doi:10.1186/gb-2010-11-5-r54
Published: 19 May 2010Additional files
Additional file 1:
Table listing RNA half-lives and decay times for the whole transcriptome of P. marinus strain MED4. Standard errors for half-lives and decay times are presented in columns H and J. For the decay times the lower (column K) and upper (column L) bounds of error intervals are also given.
Format: PPT Size: 134KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 2:
Figure comparing microarray and quantitative RT-PCR expression profiles for 17 selected genes. The top panel compares microarray expression signals (MA; [microarray signal intensity of expression]) and quantitative RT-PCR expression signals (qPCR; [normalized to 100% at maximum]) of biological triplicates. The lower panel shows expression profiles for biological triplicates determined by microarrays (red line) and quantitative RT-PCR (black lines; note for series B two samples at time point 2.5 minutes (in grey) are illustrated).
Format: PPT Size: 82KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 3:
Table with estimates of half-lives and decay rates of genes organized in operons and their cluster membership.
Format: PPT Size: 147KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 4:
Figure displaying the relationship between the gene position within an operon and (a) half-life or (b) decay rate.
Format: PPT Size: 446KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 5:
Figure showing the relationship between single probe positions of genes with a size of at least 2 kb (monocistrons and first genes in operons) and (a) half-life or (b) decay rate.
Format: XLS Size: 539KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Table that compares computationally predicted operons from [41] with operon assignment based on this study.
Format: XLS Size: 47KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 7:
Figure comparing transcript profiles of cells treated with rifampicin dissolved in water or DMSO. RNA expression levels were determined by quantitative real-time PCR and compared to microarray data (MA) for transcripts with the regular exponential decay profiles (representing the majority of the transcriptome) that have very short half-lives: (a) recA and (b) PMM1077 and (c-e) transcripts from the type II atp operon.
Format: XLS Size: 34KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 8:
Table with information on oligonucleotides used for quantitative RT-PCR.
Format: XLS Size: 26KB Download file
This file can be viewed with: Microsoft Excel Viewer
