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Items: 1 to 20 of 103

1.

Co-immunoprecipitation of the small DUF1127 protein RSP_6037xFLAG and pRK0557_3xFLAG for RNA interaction

(Submitter supplied) Many protein domains are conserved among different classes and are found in numerous species, but their function remains obscure. Data bases list more than 17,000 DUF1127 proteins but to date no biological function could be assigned to any of these proteins. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in the maturation of the CcsR sRNAs that are processed from the 3´ UTR of the ccaF mRNA and have a role in the oxidative stress defense. more...
Organism:
Rhodobacter sphaeroides 2.4.1
Type:
Other
Platform:
GPL28141
4 Samples
Download data: CSV, WIG
2.

Transcriptome analysis of Rhodobacter sphaeroides 2.4.1 wildtype and the two overexpressing strains OE_RSP_6037 and OE_CcsR

(Submitter supplied) Many protein domains are conserved among different classes and are found in numerous species, but their function remains obscure. Data bases list more than 17,000 DUF1127 proteins but to date no biological function could be assigned to any of these proteins. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in the maturation of the CcsR sRNAs that are processed from the 3´ UTR of the ccaF mRNA and have a role in the oxidative stress defense. more...
Organism:
Cereibacter sphaeroides
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24048
9 Samples
Download data: CSV
Series
Accession:
GSE144523
ID:
200144523
3.

A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...
Organism:
Streptococcus pneumoniae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23797
22 Samples
Download data: WIG
Series
Accession:
GSE138732
ID:
200138732
4.

An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Helicobacter pylori
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19488 GPL19489
10 Samples
Download data: WIG
Series
Accession:
GSE63834
ID:
200063834
5.

An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA (RIP-seq)

(Submitter supplied) In this study several putative targets of the RRM protein RbpH (HP0827/HPG27_786) were identified. RNA binding targets of RbpH in two strains of H. pylori (G27 and 26695) were identified using RIP-seq.
Organism:
Helicobacter pylori
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19489 GPL19488
6 Samples
Download data: WIG
Series
Accession:
GSE63833
ID:
200063833
6.

An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA (RNA-seq)

(Submitter supplied) In this study several putative targets of the RRM protein RbpH (HPG27_786) were identified. Potential targets of RbpH in H. pylori (G27) were identified using total RNA-seq.
Organism:
Helicobacter pylori
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19488
4 Samples
Download data: WIG
Series
Accession:
GSE63832
ID:
200063832
7.

Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies

(Submitter supplied) Sulfurospirillum multivorans is one of the few bacteria, which can anaerobically respire organohalides such as tetrachloroethene. The regulation of this organohalide respiration is in most parts unknown. Sulfurospirillum multivorans was shown to downregulate the expression of organohalide respiration-specific genes slowly when no substrate is present, over the time of approximately 100 generations. To unravel the molecular details of this peculiar regulation and the involved factors, we sequenced the primary transcriptome of the organism.
Organism:
Sulfurospirillum multivorans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27633
8 Samples
Download data: WIG
Series
Accession:
GSE139083
ID:
200139083
8.

MM_0565 orchestrates CRISPR-based immunity in Methanosarcina mazei by transcriptional regulation of components essential for the adaptation

(Submitter supplied) CRISPR loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 of Methanosarcina mazei Gö1 associated to the type I-B CRISPR-locus providing evidence for its relevance in regulating this system. more...
Organism:
Methanosarcina mazei Go1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28591
4 Samples
Download data: TSV, WIG
Series
Accession:
GSE151372
ID:
200151372
9.

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

(Submitter supplied) Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading organism with respect to global bacterial protein-protein networks. However, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ~85% of all E. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
22 Samples
Download data: WIG
Series
Accession:
GSE152974
ID:
200152974
10.

IL-12 From Endogenous cDC1, and Not Vaccine DC, Is Required for Th1 Induction

(Submitter supplied) In this study, we generated a chimeric situation by injection of different gene-modified BM-DCs into different strains of gene-modified recipient mice. This allowed us to identify the separate functional contributions of injected versus endogenous DCs for Th1 polarization. We identified the cellular source of IL-12p70 production after subcutaneous BM-DC vaccination as endogenous migratory XCR1+ bystander DCs in the skin draining lymph nodes. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
21 Samples
Download data: CSV
Series
Accession:
GSE124677
ID:
200124677
11.

RNA-seq of S. meliloti strain ectopically overexpressing trpL and RIP-seq with 3xFLAG-tagged peptide peTrpL from S. meliloti

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Sinorhizobium meliloti
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25460
15 Samples
Download data: WIG
Series
Accession:
GSE118689
ID:
200118689
12.

Analysis of RNA coimmunoprecipitated with 3xFLAG-tagged peptide peTrpL from Sinorhizobium meliloti

(Submitter supplied) We show that specific RNAs are coimmunoprecipitated in a tetracycline-dependent manner with the Flag-tagged peptide peTrpL of S. meliloti
Organism:
Sinorhizobium meliloti
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25460
6 Samples
Download data: WIG
Series
Accession:
GSE118688
ID:
200118688
13.

Transcriptome analysis of Sinorhizobium meliloti strain ectopically overexpressing trpL

(Submitter supplied) We show that the RNA leves of many genes in the S. meliloti overexpressing strain (OE) 2011 (pRK-RcsR1) are more similar to the levels of in wild type (WT) strain 2011 than in the empty vector control (EVC) strain 2011(pRK4352). Since the plasmid-containing strains were grown in the presence of 10 µg/ml tetracycline (Tc), while the WT was grown without Tc, the results suggest that the intrecellular Tc concentration in the OE strain are lower than in the EVC. more...
Organism:
Sinorhizobium meliloti
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25460
9 Samples
Download data: WIG
Series
Accession:
GSE118687
ID:
200118687
14.

Global identification of RNase E sites in Vibrio cholerae

(Submitter supplied) In this study, we employed TIER-seq in V. cholerae to identify cleavage sites of RNase E on a genome-wide scale.
Organism:
Vibrio cholerae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL25005
12 Samples
Download data: CSV, WIG
Series
Accession:
GSE148675
ID:
200148675
15.

OppZ target identification

(Submitter supplied) In this study we determined the target spectrum of the Vibrio cholerae OppZ sRNA via pulse-expression followed by RNA-sequencing.
Organism:
Vibrio cholerae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25180
6 Samples
Download data: XLSX
Series
Accession:
GSE144479
ID:
200144479
16.

Identification of bicyclomycin-sensitive transcripts in Vibrio cholerae

(Submitter supplied) In this study we used BCM, inhibitor of Rho activity, to determine Rho-dependent transcription termination sites in V. cholerae.
Organism:
Vibrio cholerae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25005
12 Samples
Download data: XLSX
Series
Accession:
GSE144478
ID:
200144478
17.

Exonuclease-mediated sRNA activation in competence regulation in a Gram-positive bacterium

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Streptococcus pneumoniae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL23797
28 Samples
Download data: WIG
Series
Accession:
GSE145605
ID:
200145605
18.

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...
Organism:
Streptococcus pneumoniae
Type:
Other
Platform:
GPL23797
6 Samples
Download data: WIG
19.

Different Campylobacter species show variances in their heat stress response

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Campylobacter lari; Campylobacter coli
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19975 GPL19973
8 Samples
Download data: WIG
Series
Accession:
GSE67486
ID:
200067486
20.

Different Campylobacter species show variances in their heat stress response [Campylobacter lari]

(Submitter supplied) Background: The food-borne pathogen Campylobacter is one of the most important zoonotic pathogens. Compared to other zoonotic bacteria, Campylobacter species are quite susceptible to environmental or technological stressors. This might be due to the lack of many stress response mechanisms described in other bacteria. Nevertheless, Campylobacter is able to survive in the environment and food products. more...
Organism:
Campylobacter lari
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19975
4 Samples
Download data: WIG
Series
Accession:
GSE67468
ID:
200067468
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