GEO DataSets

(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) 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) Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. more...

Organism:

Candida albicans

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10636 GPL10637

12 Samples

Download data: TXT

(Submitter supplied) Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16611

1 Sample

Download data: TXT

(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 venezuelae; Streptomyces coelicolor; Streptomyces avermitilis

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) We used this array as described in Babak, Blencowe, anf Hughes (2005), to screen novel ncRNA predictions. See author supplementary data for more detailed probe information. Keywords: parallel sample

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL1896

16 Samples

Download data

(Submitter supplied) Expression profiling of multiple mouse tissues against 57931 RIKEN cDNAs Keywords: dual color nucleotide, tissue comparison

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL2733 GPL2734 GPL2732

256 Samples

Download data

(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) We deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harbouring CARS.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9052

1 Sample

Download data: TXT

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21117

75 Samples

Download data: BED, BW

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21117

3 Samples

Download data: BED

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

36 Samples

Download data: BW

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

36 Samples

Download data: BW