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Links from GEO DataSets

Items: 17

1.

Saccharopolyspora erythraea RNA-seq

(Submitter supplied) We report the high-throughput profiling of saccharopolyspora erythraea including a industrial strain HL3168 E3 and a wild-type strain NRRL23338. The aim was to evaluate the difference in expression of sRNA predicted in silico related to secondary metabolites in Saccharopolyspora erythraea.
Organism:
Saccharopolyspora erythraea
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17450
2 Samples
Download data: TXT
Series
Accession:
GSE48887
ID:
200048887
2.

Physiological responses of Saccharopolyspora erythraea towards perturbation of intracellular ATP

(Submitter supplied) Saccharopolyspora erythraea is used for industrial-scale production of erythromycin. To explore the physiological role of co-factors in regulation of primary and secondary metabolism of S. erythraea, we initially overexpressed the endogenous F1-ATPase in an erythromycin high-producing strain, E3. The engineered strain is named EA. The F1-ATPase expression resulted in a lower [ATP]/[ADP] ratio, which was accompanied by a dramatic increased production of a reddish pigment and a decreased erythromycin production. more...
Organism:
Saccharopolyspora erythraea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26951
8 Samples
Download data: TSV
Series
Accession:
GSE134767
ID:
200134767
3.

Transcriptome analysis of wild type and erythromycin-producing strain of S. erythraea

(Submitter supplied) Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. We used transcriptomic approach to compare whole genome expression in erythromycin high-producing strain, compared to the wild type S. erythraea strain in four stages of fermentation.
Organism:
Saccharopolyspora erythraea
Type:
Expression profiling by array
Platform:
GPL19656
22 Samples
Download data: TXT
Series
Accession:
GSE65007
ID:
200065007
4.

Next Generation Sequencing Facilitates Putative Target Identification for the Small RNA RydC

(Submitter supplied) We report the transcriptomic profile of Escherichia coli when the small RNA RydC is overexpressedand how this can be used to identify putative mRNA targets. This technique allowed us to identify potential mRNA targets to further validate in vivo.
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15010
6 Samples
Download data: TXT, WIG
Series
Accession:
GSE121595
ID:
200121595
5.

Comparative Genomics Reveals New Molecular targets for Accelerated Improvement of Erythromycin-producing Strains

(Submitter supplied) Information about molecular mechanisms underlying improvement of antibiotic-producing microorganisms with traditional mutation and screening approach is largely missing. This information is essential to develop rational approaches to strain improvement. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. more...
Organism:
Saccharopolyspora erythraea
Type:
Expression profiling by array
Platform:
GPL6051
22 Samples
Download data: CEL, CHP
Series
Accession:
GSE30600
ID:
200030600
6.

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

(Submitter supplied) In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. more...
Organism:
Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19476
4 Samples
Download data: XLS
Series
Accession:
GSE74936
ID:
200074936
7.

Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

(Submitter supplied) We present the first genome-wide identification and characterizaion of 422 novel sRNAs in R. capsulatus. In addition we report a comparative analysis of conserved sRNAs across 24 bacterial species.
Organism:
Rhodobacter capsulatus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL20771
2 Samples
Download data: XLS
Series
Accession:
GSE82056
ID:
200082056
8.

Small RNA Sequencing of the Plant Growth Promoting Bacterium Azospirillum brasilense Sp245

(Submitter supplied) Small RNAs are the non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs that has been carried out in various plant growth promoting bacteria have shown to help the bacterial cell cope up with environmental stress. more...
Organism:
Azospirillum baldaniorum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL25390
2 Samples
Download data: TXT
Series
Accession:
GSE117764
ID:
200117764
9.

Transcriptome analysis and 3‘-end detection of total RNA from Rhodobacter sphaeroides 2.4.1 wildtype, polynucleotide phosphorylase (pnp) mutant and RNase III (rnc) mutant strain

(Submitter supplied) The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. more...
Organism:
Cereibacter sphaeroides
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24048
9 Samples
Download data: BED, CSV, WIG
Series
Accession:
GSE156818
ID:
200156818
10.

Investigating the sRNA and mRNA transcriptional response to antibiotics in methicillin-resistant Staphylococcus aureus using Illumina RNAseq

(Submitter supplied) Coordinated protein-coding sequence transcriptional responses of Staphylococcus aureus to antimicrobial exposure are well described but little is known of the role of bacterial non-coding, small RNAs (sRNAs) in these responses. Here we used RNAseq to investigate the sRNA response of the epidemic multiresistant hospital ST239 S. Aureus strain JKD6009 and its vancomycin-intermediate clinical derivative, JKD6008, after exposure to four antibiotics representing the major classes of antimicrobials used to treat methicillin-resistant S. more...
Organism:
Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16057
40 Samples
Download data: CSV, TXT
Series
Accession:
GSE40864
ID:
200040864
11.

Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis

(Submitter supplied) Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. more...
Organism:
Staphylococcus epidermidis; Staphylococcus aureus; Staphylococcus carnosus
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL21408 GPL19476 GPL21407
3 Samples
Download data: XLSX
Series
Accession:
GSE77567
ID:
200077567
12.

Transcriptional profile (mRNA and sRNA) of Clostridium acetobutylicum to metabolite stress, butanol and butyrate

(Submitter supplied) The transcription profile of C. acetobutylicum to two major metabolite stress, butanol and butyric acid, was comprehensively investigated at three different concentrations of each metabolite and at four different time points (15, 30, 60 and 75 min post stress). All experiments were performed in 3 parallel biological replicates and the RNA extraction was perfomed in a manner to retain the small RNAs and hence, investigate their role and expression under stress.
Organism:
Clostridium acetobutylicum
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17364
84 Samples
Download data: TXT
Series
Accession:
GSE48349
ID:
200048349
13.

Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae

(Submitter supplied) The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. more...
Organism:
Oryza sativa; Pyricularia oryzae
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL9316 GPL16451
8 Samples
Download data: TXT
Series
Accession:
GSE43277
ID:
200043277
14.

Identification of target genes differentially expressed after pulse expression of Neisseria gonorrhoeae sRNAs

(Submitter supplied) Purpose: The goal of this study was the identification of target genes of the Neisseria gonorrhoeae sRNAs NgncR_237, NgncR_162 and NgncR_163. Methods: RNA was isolated from N. gonorrhoeae using the miRNeasy Micro Kit (Qiagen). Enrichment of mRNA was done using the Universal Ribodepletion Kit followed by Next Ultra Directional Library Preparation Kit for Illumina (NEB). The cDNA was sequenced on Illumina HiSeq 3000 platform with 100 bp paired end reads. more...
Organism:
Neisseria gonorrhoeae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30262
18 Samples
Download data: CSV
Series
Accession:
GSE177032
ID:
200177032
15.

Distinct small RNA populations act antagonistically in formation of heterosis

(Submitter supplied) This research reports the analysis of sRNAs in 14 and 7 inbred lines from a breeding population. We analyzed the contribution of sRNAs to the formation of heterosis via integrative association analysis with field data of 98 hybrids generated from the set of inbred lines. Our results indicate a contribution of sRNAs to heterosis. We were able to identify different sets of sRNAs associated with heterosis with distinct length and genome distribution patterns.
Organism:
Zea mays
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15463
25 Samples
Download data: TXT
Series
Accession:
GSE51662
ID:
200051662
16.

Genome-wide analysis of gene expression profiles of 21 European maize (Zea mays L.) inbred lines.

(Submitter supplied) In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. more...
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL6438
63 Samples
Download data: GPR
Series
Accession:
GSE17754
ID:
200017754
17.

CRISPR-based screening of small RNA modulators of bile susceptibility in Bacteroides thetaiotaomicron

(Submitter supplied) Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota member Bac-teroides thetaiotaomicron for genome-wide sRNA screens. more...
Organism:
Bacteroides thetaiotaomicron
Type:
Other
Platforms:
GPL33520 GPL28094
9 Samples
Download data: FASTA, TXT
Series
Accession:
GSE235620
ID:
200235620
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