RIBOBASE

Welcome to Salmonella Typhimurium SL1344

Introduction

This section contains Ribo-seq datasets for the pathogenic bacterium Salmonella Typhimurium, generated in collaboration with Prof. Jörg Vogel from the University of Würzburg, Germany. Ribo-seq datasets were prepared for the wild-type Salmonella Typhimurium grown in rich medium (LB), SPI-1, and SPI-2-inducing conditions.

Publication

The publication describing this project can be accessed via the following DOI: https://doi.org/10.1093/femsml/uqaa002

Data availability

The raw sequencing data used in this study can be accessed via the GEO accession number GSE149893.

TraDIS data that support the finding of the study can be accessed via the GEO accession number GSE149580.

RNA-seq data that support the finding of the study can be accessed via the GEO accession number GSE149928.

The Mass spectrometry data is available on ProteomeXchange: PXD018754.

The Mass spectrometry from GradR data is available on ProteomeXchange: PXD018422.

The processed files used in this JBrowse2 genome browser can be downloaded here.

JBrowse2

Access Area

Default session

Access JBrowse

Annotation tracks

We provide multiple annotation tracks for the Salmonella Typhimurium SL1344 genome.
All annotation files can be loaded and unloaded using their respective check box in the track selector.
Annotation files are indexed and specific genes can be searched by gene name, locus tag or gene id using the search box in the top center of the JBrowse2 instance.
This JBrowse2 instance includes:

Track	Description
The Reference Annotation	The reference annotation for Salmonella Typhimurium SL1344
Refseq Annotation (23.12.2022)	The Refseq annotation for Salmonella Typhimurium SL1344
DeepRibo Predictions	A list of ORF predictions created using the tool DeepRibo.
Reparation Predictions	A list of ORF predictions created using the tool Reparation.
Novel sORFs (Ribo-seq)	A list of novel sORFs discovered using Ribo-seq data.
Novel sORFs (sPepFinder)	A list of novel sORFs discovered using sPepFinder.
Start Codon Motifs	All ATG motifs for the reference genome.
Alternative Start Codon Motifs	All GTG and TTG motifs for the reference genome.
Stop Codon Motifs	All TAA, TAG and TGA motifs for the reference genome.
RBS Motif	All AAGG motifs for the reference genome.

Coverage tracks

Coverage tracks show the normalized read counts per nucleotide position. There are multiple mapping types used (threeprime/fiveprime/global). The mapping method of each file is marked in their description.

Shareable Links

JBrowse2 allows you to easily share observations with your colleagues and collaborators.
Using the "share"-button next to the session name, you can automatically generate a link. Anyone that uses this link will see the exact session you are currently looking at. This includes colors, zoom level, scale, loaded tracks etc...
This is a very powerful tool for sharing potential discoveries.

JBrowse2 user guide

For more information on how to use JBrowse2, please have a look at the comprehensive user guide provided by the JBrowse team. The chapter on basic usage is highly recommended to get familiar with the JBrowse2 interface.