CampyBrowse

CampyBrowse includes data from our three translatomics experiments ( Exp1, Exp2, Exp3; Froschauer, Svensson et al. submitted) and dRNA-seq (Dugar et al. 2013), For quick browsing, we provide four pre-set JBrowse sessions for 1) dRNA-seq & Ribo-seq, 2) Ribo-seq & TIS profiling, 3) Ribo-seq & TIS/TTS profiling, and 4) all translatomics experiments as described below. All data was generated in standard growth conditions (log phase (OD₆₀₀~0.5), rich medium (Brucella broth), microaerobic atmosphere) in the wild-type (WT) strain, unless otherwise noted.

For detailed instructions on how to use CampyBrowse, developed using JBrowse (Buels et al. 2016) see our README.

Our custom annotation used for the analysis can be downloaded here.
An annotation updated based on translatomics can be downloaded here.

🢒 Please Note:

All datasets are available in the different pre-sets. They are just not loaded on initial opening, but they can be loaded using the track-selector.

Pre-Set 1: dRNA-seq & Ribo-seq

Differential RNA-seq (dRNA-seq) was used to map transcription start sites based on enrichment in +TEX vs. -TEX libraries. In addition, full-read coverage for Ribo-seq (ribosome footprints) and parallel RNA-seq (total RNA) is provided for identification of translated genes.

Pre-Set 2: Ribo-seq & TIS (translation initiation site) profiling

TIS profiling (Weaver et al., 2019; Meydan et al., 2019) and parallel Ribo-seq data identify ORFs and strat codons. To stall ribosomes at TIS, cultures were treated with Ret (retapamulin; Exp2) or Onc (oncocin; Exp3). Tracks display coverage for 3'-end positions of reads only; TIS peaks are expected at ~16/17 nt (Ret/Onc, respecitvely) downstream of start codons. Peaks are generally enriched in the TIS vs. Ribo-seq (no drug) library. RNA- and Ribo-seq with full-read mapping is also displayed. For Exp2 (TIS(Ret)), a ΔcmeB strain (efflux pump mutant) was used.

Pre-Set 3: Ribo-seq, TIS & TTS (translation termination site) profiling

This environment provides data from all translatomics approaches to reveal ORFs and their boundaries (start and stop codons). For TTS, ribosomes were stalled at stop codons with apidaecin (Api) (Mangano et al. 2020) and includes libraries generated from monosomes [TTS(Mono)] and disome [TTS(Di)] footprints from collisions at stop codons. A parallel TIS (Onc) library can be used to identify start codons, where Api might also enrich ribosomes. Tracks show either 5' or 3'-end mapping. For 3' ends, a peak (for TTS(Mono), enriched in TTS vs. Ribo-seq/TIS) is expected ~13 nt downstream of stop codons. For 5' ends ([TTS(Di)] only), a peak is expected ~45 nt upstream of the stop codons. RNA- and Ribo-seq with full-read mapping is also displayed.

Pre-Set 4: All translatomics datasets

This environment provides data from all translatomics experiments to reveal ORFs and their boundaries (start and stop codons).

Collaborators

Funding

Citations:

1) Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, et al. (2013) High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates. PLOS Genetics 9(5): e1003495.

2) Froschauer K^*, Svensson SL^*, et al. Complementary Ribo-seq approaches refine the translatome and provide a small protein census in Campylobacter jejuni. submitted

3) Buels, Robert, et al. "JBrowse: a dynamic web platform for genome visualization and analysis." Genome Biology 17.1 (2016): 66.

4) Weaver J, Mohammad F, Buskirk AR, Storz G. Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes. mBio.

5) Meydan S, Marks J, Klepacki D, Sharma V, Baranov PV, Firth AE, Margus T, Kefi A, Vázquez-Laslop N, Mankin AS. Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell. 74: 481-493.e6.