GEO DataSets

(Submitter supplied) Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. more...

Organism:

Bartonella henselae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16712

4 Samples

Download data: TSV

(Submitter supplied) The delineation of genes in bacteria has remained an important challenge because prokaryotic genomes are often tightly packed frequently resulting in overlapping genes. We hereby present a de novo approach called REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION) to delineate translated open reading frames (ORFs) in bacteria independent of (available) genome annotation. By deep sequencing of ribosome protected mRNA fragments (RPF) to map translating ribosomes across the entire genome, REPARATION takes advantage of the recently developed ribosome profiling (Ribo-seq) technique. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20056

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20219

4 Samples

Download data: WIG

(Submitter supplied) With a view to re-annotate the genome sequence of the nitrogen fixing bacterium Sinorhizobium meliloti, we generated oriented sequences of transcripts. To cover a large number of expressed genes we prepared RNA from bacteria grown in three very different physiological conditions including bacteria grown in liquid cultures (in both exponential and stationary growth phases) and from 10-day-old nodules in which bacteria were differentiated in nitrogen fixing bacteroids. more...

Organism:

Sinorhizobium meliloti; Medicago truncatula

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16595 GPL16596

18 Samples

Download data: TXT

(Submitter supplied) Proteogenomics is an emerging research field yet lacking a standard method of analysis. In this article, we demonstrate the strength of proteogenomic analysis specific for N-terminal data that aims at the discovery of novel translational start sites. In summary, unidentified spectra were matched to a specific N-terminal peptide library encompassing all theoretical protein N-termini encoded in the genome. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BEDGRAPH

(Submitter supplied) We developed a novel algorithm, smORFer, detecting smORFs (e.g. <50 codons) which performs with higher accuracy in prokaryotic organisms. smORFer considers structural features of genetic sequence along with in-register translation and using Fourier transform converts them into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way and dependent on the data available different modules can be tested.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19006

2 Samples

Download data: TXT

(Submitter supplied) The study aims to to determine temperature sensitive genes across the strains COW5,PBIB15 and pestoidesF.

Organism:

Yersinia pestis; Yersinia pestis CO92

Type:

Expression profiling by array

Platform:

GPL9009

24 Samples

Download data: MEV

(Submitter supplied) Ribosome profiling was applied for the first time on S. meliloti to generate a translatome map. Our work reveals active translation for several ORFs including small ORFs (sORFs). In addition, our ribosome profiling data led to the discovery of several translated non-annotated sORFs. Translation of these non-annotated sORFs was validated by proteomics and western blotting.

Organism:

Sinorhizobium meliloti 2011

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL32373

4 Samples

Download data: BW

(Submitter supplied) The genome sequence is the “blue-print of life”, but proteomics is required to relate this blue-print of life to the actual physiology of living cells. Because of their low complexity – only about 2.000 proteins make a Staphylococcus aureus cell viable – bacteria are excellent model systems to identify the entire protein assembly of a living organism. Many of the studies on physiological proteomics of bacteria, however, still rely on 2D gel-based technologies that visualize only a minor part of the proteome. more...

Organism:

Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL7137

4 Samples

Download data: TXT

(Submitter supplied) Streptococcus pyogenes growth-phase dependent and Rgg-dependent transcription was analyzed Keywords: transcriptional regulation

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL3312

9 Samples

Download data

(Submitter supplied) Background: Previous studies comparing quantitative proteomics and microarray data have generally found poor correspondence between the two. We hypothesised that this might in part be because the different assays were targeting different parts of the expressed genome and might therefore be subjected to confounding effects from processes such as alternative splicing. Results: Using a genome database as a platform for integration, we combined quantitative protein mass spectrometry with Affymetrix Exon array data at the level of individual exons. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

6 Samples

Download data: CEL