GEO DataSets

(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) In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. more...

Organism:

Botrytis cinerea; Botrytis paeoniae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL22004 GPL22005

3 Samples

Download data: TXT

(Submitter supplied) Aspergillus fumigatus is an important human pathogen and a leading fungal killer. This study aimed to determine the small RNA repertoire of A. fumigatus in conidia and mycelium grown for 24 or 48 hours in liquid culture.

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28001

9 Samples

Download data: XLSX

(Submitter supplied) The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. more...

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33056

36 Samples

Download data: XLSX

(Submitter supplied) Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. more...

Organism:

Bombus terrestris

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19585

8 Samples

Download data: CSV

(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 found a new population of 31nt sRNAs that results from the addition of a non-templated 3-4 adenosine nucleotides at the 3´-end of the 27nt sRNA populations. We sequenced various sRNA libraries including both total RNAs and IP-ed RNAs of EhAgo proteins.

Organism:

Entamoeba histolytica; Entamoeba invadens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL19934 GPL19933

13 Samples

Download data: TXT

(Submitter supplied) Dendritic cells were infected with human cytomegalovirus (CMV) for 4, 8 or 12 hours. Single-cultures of dendritic cells serve as controls. RNA was isolated and processed for next generation sequencing.

Organism:

Homo sapiens; Human betaherpesvirus 5

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24958 GPL18573

7 Samples

Download data: TSV

(Submitter supplied) Dendritic cells and A. fumigatus were co-cultured with two different MOIs (1 or 0,5) for 2, 4 or 6 hours. Single-cultures of dendritic cells and A. fumigatus serve as controls. RNA was isolated and processed for next generation sequencing.

Organism:

Aspergillus fumigatus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23268 GPL26921 GPL18573

12 Samples

Download data: TSV

(Submitter supplied) Human dendritic cells were coinfected with Aspergillus fumigatus and human cytomegalovirus. Single-cultures or single-infections served as controls. RNA was isolated and processed for next generation sequencing.

Organism:

Homo sapiens; Human betaherpesvirus 5; Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

40 Samples

Download data: TSV

(Submitter supplied) Here we determine the impact upon the loss of M-2 dsRNA alone and both L-A-lus along with M-2 on the host S. cerevisiae transcriptional changes. By performing profiling of the whole transcriptomes, we determined 486 genes differentially expressed after curing of yeast cells from M-2 dsRNA and 715 genes affected by the elimination of both M-2 and L-A-lus dsRNAs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17582

9 Samples

Download data: TXT

(Submitter supplied) Transcriptome analysis of small RNA was performed using pollen and embryonic callus, and vegetative tissues, needles of Picea abies to address differences in small RNA profiles between reproductive tissues and vegetative tissues in gymnosperm.

Organism:

Picea abies

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19695

10 Samples

Download data: TXT

(Submitter supplied) A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

55 Samples

Download data: TXT

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

Organism:

Nicotiana benthamiana; Cymbidium ringspot virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15026 GPL10313

6 Samples

Download data: FNA, QUAL

(Submitter supplied) We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation-based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. more...

Organism:

Nicotiana benthamiana; Cymbidium ringspot virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15026

2 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation-based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. more...

Organism:

Nicotiana benthamiana; Cymbidium ringspot virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10313

4 Samples

Download data: TXT

(Submitter supplied) We reported the small RNA profiles of disease free and SLCMV infected leaves of susceptible and tolerant genotypes of cassava. The sRNA data generated through high throughput small RNA sequencing revealed critical regulatory role of host and pathogen derived small RNAs during SLCMV infection.

Organism:

Manihot esculenta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21982

3 Samples

Download data: FA

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

Organism:

Fusarium fujikuroi; Fusarium oxysporum f. sp. lycopersici

Type:

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

Platforms:

GPL24816 GPL22633 GPL34083

14 Samples

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(Submitter supplied) RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. more...

Organism:

Fusarium fujikuroi; Fusarium oxysporum f. sp. lycopersici

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL34083 GPL22633

8 Samples

Download data: CSV