Datasets used for TSS-Captur

Three processed datasets that can be used as an input for the pipeline TSS-Captur, containing a MasterTable computed using TSSpredator, the corresponding FASTA file and the annotation file (in form of a GFF file). A short description of the datasets follows:

scoelicolor.zip: Contains the input data used for the report presented in the manuscript for TSS-Captur. The study uses the data by Jeong, et al. (2016), where Streptomyces coelicolor analyzed under different conditions. For more information, refer to the original study. 

cjejuni.zip: A further dataset for usage in TSS-Captur. Contains the data of a study comparing the transcriptome of four different strains of Campylobacter jejuni (Dugar, et al., 2013) using TSSpredator to compute a genome-wide TSS map.

bacteroides_plasmid.zip: A small dataset based on the study by Ryan, et al. (2020), where the transcriptome of Bacteroides thetaiotaomicron was analyzed. The MasterTable was produced using TSSpredator and very sensitive parameters. 

References: 

Dugar, G., Herbig, A., Förstner, K. U., Heidrich, N., Reinhardt, R., Nieselt, K., & Sharma, C. M. (2013). High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS genetics, 9(5), e1003495.

Jeong, Y., Kim, J. N., Kim, M. W., Bucca, G., Cho, S., Yoon, Y. J., ... & Cho, B. K. (2016). The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3 (2). Nature communications, 7(1), 11605.

Ryan, D., Jenniches, L., Reichardt, S., Barquist, L., & Westermann, A. J. (2020). A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Nature communications, 11(1), 3557.