GEO DataSets

(Submitter supplied) We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters.

Organism:

Streptomyces coelicolor; Streptomyces avermitilis; Streptomyces venezuelae

Type:

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

Platforms:

GPL17014 GPL17012 GPL17013

6 Samples

Download data: TXT

(Submitter supplied) 89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions.

Organism:

Rhizobium etli CFN 42

Type:

Non-coding RNA profiling by genome tiling array; Expression profiling by genome tiling array

Platform:

GPL9409

5 Samples

Download data: GFF, TXT

(Submitter supplied) In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15856

2 Samples

Download data: BED

(Submitter supplied) Intermediate-size noncoding RNAs (is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Plasmodium falciparum, which is the most virulent malaria parasite infecting human being. By using Illumina/Solexa paired-end sequencing of an is-ncRNA-specific library, we performed a systematic identification of novel is-ncRNAs in intraerythrocytic P. more...

Organism:

Plasmodium falciparum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16789

1 Sample

Download data: TXT

(Submitter supplied) To understand functional roles of ncRNAs during exponential growth phase, we captured transcriptome changes by conducting strand-specific RNA-seq.

Organism:

Kluyveromyces marxianus

Type:

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

Platform:

GPL20596

6 Samples

Download data: GFF, TXT

(Submitter supplied) Comparative hybridization of wild type versus AdpA deficient mutant Keywords: Cell type comparison

Organism:

Streptomyces griseus; Streptomyces griseus subsp. griseus NBRC 13350

Type:

Expression profiling by array

Platform:

GPL5473

4 Samples

Download data: TXT

(Submitter supplied) Legionella pneumophila is a Gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila in broth growth and in infection of A. more...

Organism:

Legionella pneumophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13156

5 Samples

Download data: BED

(Submitter supplied) Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. more...

Organism:

Listeria monocytogenes EGD-e; Listeria innocua Clip11262

Type:

Other

Platforms:

GPL15272 GPL15273

16 Samples

Download data: TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) afsS::apr mutant strain (YSK4425) and compare it to wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

23 Samples

Download data: GPR

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

22 Samples

Download data: GPR

(Submitter supplied) Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in such studies, instances of divergent trends are frequently observed indicating the existence of post-transcriptional regulation. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

12 Samples

Download data: GPR

(Submitter supplied) Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of orthology. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle yet crucial differences between these two chromosomes. more...

Organism:

Streptomyces coelicolor; Streptomyces lividans

Type:

Genome variation profiling by array

Platform:

GPL4908

3 Samples

Download data: GPR

(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) Small RNA and regulatory RNA discovery has been based on (i) computational predictions mainly in intergenic regions, (ii) microarray experiments, (iii) shotgun cloning of cDNA libraries, (iv) classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels and (v) copurification with proteins like Hfq, CsrA and RNA polymerase. In this study, we attempted to experimentally validate in silico small and regulatory RNA predictions for V. more...

Organism:

Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

Type:

Expression profiling by array

Platform:

GPL10230

5 Samples

Download data: CEL

(Submitter supplied) Methods: RNA profiles of 12 tissues were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: This work has focused on identification of non-coding RNAs expressed in human tissues. We have identified a set of non-coding RNAs that are both expressed and conserved, as described in the manuscript accompagnying this work.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: GTF

(Submitter supplied) Thousands of novel non-coding RNAs (ncRNA) has been identified in recent years. Only few have been functionally characterized and it is thus unclear which and how many are functional. Here, we characterize expression of ncRNAs in twelve human tissues using a costum designed microarray. The study serve as a first analysis to gain further insight into expression behavior of a broad and comprehensive collection of ncRNAs and pinpoint a set of ncRNAs we believe are functional.

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platform:

GPL16228

36 Samples

Download data: XYS