We are excited to present our Ribo-seq datasets for the halophilic archaeon Haloferax volcanii, generated in collaboration with Prof. Anita Marchfelder from Ulm University, Germany. H. volcanii is a model organism for studying the unique adaptations of extremophiles to high-salt environments. Despite its importance, the translation of small open reading frames (sORFs) and their encoded proteins in H. volcanii remains poorly understood.

To address this knowledge gap, we established a Ribo-seq procedure for the wild-type H. volcanii H119 under standard growth conditions. Our datasets were generated at 45℃ in YPC medium during the exponential growth phase (OD_600nm 0.4). Using computational tools and manual curation, we identified several novel sORFs in the H. volcanii genome.

Our Ribo-seq datasets offer a unique opportunity to explore the translation of protein and small proteins in this important model organism. We believe that our datasets will be a valuable resource for the scientific community studying extremophiles and will advance our understanding of the biology of H. volcanii.
The original work can be found at: https://doi.org/10.1093/femsml/uqad001.

This dataset section presents Ribo-seq data for Mycobacterium tuberculosis (Wade et al.), essential for understanding tuberculosis pathology.

The study provides a comprehensive analysis of open reading frames, revealing numerous previously unknown ORFs, primarily short in length. These findings offer valuable insights into the extensive translation occurring within the M. tuberculosis transcriptome, contributing significantly to the field of tuberculosis research.
The original work can be found at: https://doi.org/10.7554/eLife.73980.

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.

The original work can be found at: 10.1093/femsml/uqaa002.

Exciting news for the scientific community interested in plant-symbiont interactions! We are thrilled to share our latest Ribo-seq datasets for Sinorhizobium meliloti, a key player in nitrogen fixation and an important partner of leguminous plants. These datasets were generated in collaboration with Prof. Elena Evguenieva-Hackenberg from the University of Giessen, Germany, and offer a unique opportunity to explore the translational landscape of this fascinating microbe.

These Ribo-seq datasets were prepared for the wild-type S. meliloti 2011 strain grown semi-aerobically at 30℃ in GMS minimal medium containing streptomycin and harvested in exponential growth phase (OD_600nm 0.5). With these datasets, you'll be able to dive deep into the translatome of S. meliloti and gain unprecedented insights into its overlooked small proteome.
The original work can be found at: https://doi.org/10.1093/femsml/uqad012 .

The food-borne pathogen Campylobacter jejuni is a microaerophilic Epsilonproteobacterium and currently the leading cause of bacterial gastroenteritis worldwide. Because its annotated genome lacks homologs of key virulence factors used by other enteric pathogens, little is known about how it causes disease. In its small genome of ~1.6 Mbp, 54 small proteins of less than 70 aa are annotated. So far almost nothing is known about their involvement in C. jejuni physiology and verification of translation is lacking for most of them. Furthermore, the C. jejuni small proteome is likely larger than what is currently annotated.

The lab of Prof. Dr. Cynthia Sharma (University of Würzburg, Germany) has applied an integrative translatomics approach to map the coding capacity of this major human pathogen.

This section showcases a valuable resource for the scientific community, providing access to high-quality Ribo-seq datasets for Methanosarcina mazei, a mesophilic methanogenic archaeon. These datasets were generated in collaboration with Prof. Ruth Schmitz-Streit from Kiel University, Germany. The Ribo-seq datasets are derived from wild-type Methanosarcina mazei strain Gö1, cultivated under both nitrogen-sufficient (Nitrogen+) and nitrogen-limited (Nitrogen-) conditions, and harvested during the exponential growth phase (OD_600nm 0.3-0.4). These datasets represent a significant contribution to the field and will undoubtedly facilitate further insights into the molecular mechanisms underlying the growth and adaptation of this unique organism.

This section offers a valuable resource to the scientific community, providing access to Ribo-seq and TIS/TTS profiling datasets for Synechocystis, a widely studied cyanobacterium. The datasets were produced in collaboration with Prof. Wolfgang Hess from the University of Freiburg, Germany. The Ribo-seq datasets were generated from wild-type Synechocystis 6803 cultivated under various growth conditions (High carbon, low carbon, nitrogen limitation, and dark), and harvested during the exponential growth phase (OD_600nm 0.4). TIS/TTS profiling datasets were obtained from wild-type Synechocystis 6803 cultivated under standard growth conditions and harvested during the exponential growth phase (OD_600nm 0.4).

These datasets represent a significant contribution to the field, enabling researchers to explore the molecular mechanisms underlying Synechocystis's adaptation to different growth environments. By offering unprecedented insights into gene annotation and translation, these datasets will help drive the development of novel strategies for enhancing the performance of cyanobacteria for biotechnological applications.

This section offers a valuable resource to the scientific community, providing access to Ribo-seq and TIS/TTS profiling datasets for Synechocystis, a widely studied cyanobacterium. The datasets were produced in collaboration with Prof. Wolfgang Hess from the University of Freiburg, Germany. The Ribo-seq datasets were generated from wild-type Synechocystis 6803 cultivated under various growth conditions (High carbon, low carbon, nitrogen limitation, and dark), and harvested during the exponential growth phase (OD_600nm 0.4). TIS/TTS profiling datasets were obtained from wild-type Synechocystis 6803 cultivated under standard growth conditions and harvested during the exponential growth phase (OD_600nm 0.4).

These datasets represent a significant contribution to the field, enabling researchers to explore the molecular mechanisms underlying Synechocystis's adaptation to different growth environments. By offering unprecedented insights into gene annotation and translation, these datasets will help drive the development of novel strategies for enhancing the performance of cyanobacteria for biotechnological applications.