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Ribosome profiling in cyanobacteria
dataset
posted on 2018-09-12, 13:35 authored by Jan Karlsen, Johannes Asplund-Samuelsson, Quentin Thomas, Michael Jahn, Paul HudsonPaul HudsonSupplemental material for "Ribosome profiling of Synechocystis reveals altered ribosome allocation at carbon starvation" by Karlsen et al., 2018 (DOI: 10.1128/mSystems.00126-18).
Legends.pdf contains the full legends, while short descriptions are shown below.
Table S1. Grubbs test for outliers in RPF RPKM data at HC and LC.
Table S2. RNA RPKM, RPF RPKM, and translational efficiencies at HC and LC.
Table S3. Intragenic PS pattern correlation between samples.
Figure S1. Puromycin incorporation reveals translation under Ci starvation.
Figure S2. Comparison and Pearson correlation of RPF RPKM under the different conditions.
Figure S3. Transcription level (mRNA) and protein synthesis rate (RPF; ribosome protected footprints) of the slr0373-slr0374-slr0376 operon in HC* (-5 min sample) and LC (24 h sample) conditions.
Figure S4. Pause score (PS) distribution for every codon in each condition.
Figure S5. Detailed view of the 5’ UTR pause score (PS) profile in each condition.
Figure S6. Average ORF pause score (PS) at 5’ and 3’ ends with different filtering of ORFs.
Figure S7. Pause score (PS) plots for (A) ssl1911 (gifA), (B) slr1834 (psaA) and (C) ssr0390 (psaK1).
Figure S8. Correlation of 5' UTR, ORF, and 3' UTR RPF RPKM, for each condition, and correlation of 5' UTR, ORF, and 3' UTR fold change (FC) in RPF RPKM from HC* (-5 min) to LC (24 h).
Figure S9. ORF pause score (PS) patterns are highly correlated between two conditions if the RPF RPKM is high.
Figure S10. Sucrose density gradient profiles of MNase digested polysomes shows elevated levels of dimerized ribosomes (100S) at LC.
Table S2. RNA RPKM, RPF RPKM, and translational efficiencies at HC and LC.
Table S3. Intragenic PS pattern correlation between samples.
Figure S1. Puromycin incorporation reveals translation under Ci starvation.
Figure S2. Comparison and Pearson correlation of RPF RPKM under the different conditions.
Figure S3. Transcription level (mRNA) and protein synthesis rate (RPF; ribosome protected footprints) of the slr0373-slr0374-slr0376 operon in HC* (-5 min sample) and LC (24 h sample) conditions.
Figure S4. Pause score (PS) distribution for every codon in each condition.
Figure S5. Detailed view of the 5’ UTR pause score (PS) profile in each condition.
Figure S6. Average ORF pause score (PS) at 5’ and 3’ ends with different filtering of ORFs.
Figure S7. Pause score (PS) plots for (A) ssl1911 (gifA), (B) slr1834 (psaA) and (C) ssr0390 (psaK1).
Figure S8. Correlation of 5' UTR, ORF, and 3' UTR RPF RPKM, for each condition, and correlation of 5' UTR, ORF, and 3' UTR fold change (FC) in RPF RPKM from HC* (-5 min) to LC (24 h).
Figure S9. ORF pause score (PS) patterns are highly correlated between two conditions if the RPF RPKM is high.
Figure S10. Sucrose density gradient profiles of MNase digested polysomes shows elevated levels of dimerized ribosomes (100S) at LC.
Figure S12. Total read count per nucleotide at gene 5’ and 3’ ends for each sample.
Text S1. Supplemental methods with details of ribosome profiling and RNAseq sample preparation.
