GEO DataSets

(Submitter supplied) Small RNAs are emerging as important molecules for cross-species communication. Thanks to available and affordable sequencing technologies it is now possible to sequence small RNAs (sRNA-Seq) present in samples of interacting organisms. A first step when analyzing sRNA-Seq of two interacting species is to determine which sequences are being produced by which organism. Due to their small size (18-30), small RNAs could easily map to both host and parasite genomes. more...

Organism:

Heligmosomoides polygyrus bakeri; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL25995

12 Samples

Download data: TXT

(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

(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

(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

(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

(Submitter supplied) BACKGROUND: The release of small non-coding RNAs (sRNAs) has been reported in parasitic nematodes, trematodes and cestodes of medical and veterinary importance. However, little is known regarding the diversity and composition of sRNAs released by different lifecycle stages and the portion of sRNAs that persist in host tissues during filarial infection. This information is relevant to understanding potential roles of sRNAs in parasite-to-host communication, as well as to inform on the location within the host and time point at which they can be detected. more...

Organism:

Meriones unguiculatus; Litomosoides sigmodontis

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL27762 GPL27761

78 Samples

Download data: CSV

(Submitter supplied) Small RNA sequencing in WT Arabidopsis tissue for analysis of miRNA expression paired with qRT-PCR data.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: TXT

(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

(Submitter supplied) We report the use of Next Generation RNA Sequencing for confirming or improving initial identification of small regulatory RNA in Staphylococcus aureus to prodive a list of the most probable RNA molecules transcribed as independent units.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19531

6 Samples

Download data: TXT

(Submitter supplied) Small RNA libraries of 4 different mycovirus-infected and -free isogenic lines of A. fumigatus were constructed using Scriptminer adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified.

Organism:

Aspergillus fumigatus

Type:

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

Platform:

GPL18295

16 Samples

Download data: CSV

(Submitter supplied) Small RNA libraries of three different mycovirus-infected A. fumigatus isolates were constructed by using Illumina high definition adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified.

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18295

3 Samples

Download data: CSV

(Submitter supplied) We report the small RNA content of extracellular vesicles (EVs) from adult parasite Trichuris muris and Heligmosomoides bakeri

Organism:

Trichuris muris; Heligmosomoides polygyrus bakeri

Type:

Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL28695 GPL25342 GPL28696

15 Samples

Download data: XLSX

(Submitter supplied) Analysis of size selected RNA samples to identify sRNAs using wild-type and rpoS mutant strains.

Organism:

Xenorhabdus nematophila

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16821

4 Samples

Download data: TXT

(Submitter supplied) We report the use of Next Generation RNA Sequencing to identifiy novel sRNAs in the human pathogen Staphylococcus aureus

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18481 GPL19531

10 Samples

Download data: TXT

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:

Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

54 Samples

Download data: TXT

(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

(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

(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

(Submitter supplied) We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during glucose-phosphate stress. In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16864

8 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was carried out on N. gonorrhoeae grown in vitro to verify accuracy of a novel RNA-seq analysis program, Rockhopper

Organism:

Neisseria gonorrhoeae F62

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16863

3 Samples

Download data: TXT