GEO DataSets

(Submitter supplied) To assess which F. tularensis LVS transcripts are impacted by loss of bS21-2, we generated cells lacking the gene encoding bS21-2 (LVS ∆rpsU2). We then grew wild-type cells containing an empty vector (LVS pF), cells lacking bS21-2 with empty vector (LVS ∆rpsU2 pF), and cells lacking the native bS21-2 but ectopically expressing bS21-2 from a plasmid (LVS ∆rpsU2 pF-rpsU2-V). We isolated RNA from mid-log phase cells and analyzed by RNA-Seq.

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32555

7 Samples

Download data: TXT

(Submitter supplied) Francisella tularensis is a Gram-negative bacterium that causes a fatal human disease known as tularemia. The Centers for Disease Control have classified F. tularensis as Category A Tier-1 Select Agent. The virulence mechanisms of Francisella are not entirely understood. Francisella possesses very few transcription regulators, and most of these regulate the expression of genes involved in intracellular survival and virulence. more...

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23586

12 Samples

Download data: XLS

(Submitter supplied) Francisella tularensis, is an extremely virulent bacterium that can be transmitted naturally by blood sucking arthropods. During mammalian infection, F. tularensis infects numerous types of host cells, including erythrocytes. As erythrocytes do not undergo phagocytosis or endocytosis, it remains unknown how F. tularensis invades these cells. Furthermore, the consequence of inhabiting the intracellular space of red blood cells has not been determined. more...

Organism:

Francisella tularensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22893

10 Samples

Download data: TXT

(Submitter supplied) The facultative intracellular bacterium Francisella tularensis causes the zoonotic disease tularemia. F. tularensis resides within host macrophages in vivo and this ability is essential for pathogenesis. The transcription factor MglA is required for expression of several Francisella genes that are necessary for replication in macrophages and for virulence in mice. We hypothesized that identification of MglA-regulated genes in the Francisella genome by transcriptional profiling of wild-type and mglA mutant bacteria would lead to the discovery of new virulence factors utilized by F. more...

Organism:

Francisella tularensis

Type:

Expression profiling by array

Platform:

GPL4062

34 Samples

Download data

(Submitter supplied) Post-transcriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode in its genome any homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. more...

Organism:

Streptococcus pneumoniae D39

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22880

6 Samples

Download data: XLS

(Submitter supplied) These microarray studies are part of a larger study characterizing a deletion mutant of the putative transcriptional regulator IclR in Francisella tularensis LVS and SchuS4 strains. The microarrays were performed using RNA isolated from wild-type LVS and a LVS iclR deletion mutant after growing in Chamberlain?s defined media pH 6.3 to early mid-log phase. Results suggest that IclR affects expression of several genes after determining statistically significant differences by SAM.

Organism:

Francisella tularensis

Type:

Expression profiling by array

Platform:

GPL5844

6 Samples

Download data: GPR, MEV

(Submitter supplied) Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

20 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. more...

Organism:

Candida albicans; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26171 GPL34036

7 Samples

Download data: MTX, TSV

(Submitter supplied) We introduce microSPLiT, a low cost and high-throughput single-cell RNA-sequencing method for gram-negative and gram-positive bacteria. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating a detailed atlas of changes in metabolism and lifestyle. We not only retrieve detailed gene expression profiles associated with known, but rare, states such as competence and PBSX prophage induction, but also identify novel and unexpected gene expression states including a heterogeneous activation of a niche metabolic pathway (myo-inositol catabolism) in a subpopulation of cells.

Organism:

Bacillus subtilis; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28092 GPL28643

3 Samples

Download data: CSV

(Submitter supplied) HLA Class I antigen processing and presentation (APP) is a highly regulated process that enables CD8+ T cell immunosurveillance. APP begins with the ribosomal synthesis of a source antigen, yet the role of ribosomes, particularly specialized ribosomes, in antigen presentation is poorly understood. Here, we show that the presence of the “P-stalk” on the ribosome enhances antigen presentation. The addition of the P-stalk to the ribosome is stimulated by cytokines that upregulate APP components, and knockdown of one of the P-stalk proteins (P1) reduces T cell recognition of tumor cells. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: TSV