GEO DataSets

(Submitter supplied) Although genome-wide transcriptional analysis has been used for many years to study bacterial gene expression, many aspects of the bacterial transcriptome remain undefined. A prominent example is antisense transcription, which has been observed in a number of bacteria, though the function of antisense transcripts, and their distribution across the bacterial genome, is still unclear. Single-stranded RNA-seq results revealed a widespread and non-random pattern of antisense transcription covering more than two-thirds of the B. more...

Organism:

Bacillus anthracis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15353

4 Samples

Download data: TXT

(Submitter supplied) In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . more...

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23263

28 Samples

Download data: TXT

(Submitter supplied) Transcription profiling of sense transcripts of 10 tissues each from human, mouse, and rat.

Organism:

Mus musculus; Homo sapiens; Rattus norvegicus

Type:

Expression profiling by array

6 related Platforms

120 Samples

Download data: CEL

(Submitter supplied) Transcription profiling of antisense transcripts of 10 tissues each from human, mouse, and rat.

Organism:

Mus musculus; Homo sapiens; Rattus norvegicus

Type:

Expression profiling by array

6 related Platforms

120 Samples

Download data: CEL

(Submitter supplied) Transcription profiling of sense and antisense transcripts of 10 tissues each from human, mouse, and rat. This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Expression profiling by array

6 related Platforms

240 Samples

Download data: CEL

(Submitter supplied) The Affymetrix GeneChip Wheat Genome Array currently provides the most comprehensive coverage of the wheat genome for a microarray. In addition to using this resource for transcript expression studies and hybridization-based DNA marker discovery, we endeavored to use the GeneChip to discover the expression of natural antisense transcript (NAT) pairs. By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. more...

Organism:

Triticum aestivum

Type:

Expression profiling by array

Platform:

GPL3802

2 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

376 Samples

Download data: TSV

(Submitter supplied) High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

353 Samples

Download data

(Submitter supplied) High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

23 Samples

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15520 GPL20795

66 Samples

Download data: BED

(Submitter supplied) We utilized the stranded RNA-seq and small RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) We utilized the targeted RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

60 Samples

Download data: BED

(Submitter supplied) We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18286

47 Samples

Download data: TXT

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

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18286 GPL18287

104 Samples

Download data: TXT

(Submitter supplied) Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including sigma factor-dependent mRNA profiling was performed to define the primary regulon of each sigma factor.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18286 GPL18287

70 Samples

Download data: CSV, PDF, TXT, XLS

(Submitter supplied) Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18286 GPL18287

34 Samples

Download data: TXT, XLS

(Submitter supplied) Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. more...

Organism:

Plasmodium vivax

Type:

Expression profiling by array

Platform:

GPL16492

2 Samples

Download data: TXT

(Submitter supplied) Sense-antisense transcript (SAT) pairs are pairs of transcripts that fully or partially overlap but are transcribed in opposite directions. Although SAT expression occurs in various species, most SAT pairs have not been examined in detail. Because our previous studies revealed some tissue specificity in SAT expression, SAT pairs might be involved in cell differentiation and the maintenance of tissue-specific gene expression programs. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL8064 GPL8065

47 Samples

Download data: TXT

(Submitter supplied) Recent bioinformatic studies revealed that many mammalian protein-coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. To analyze experimentally the incidence of antisense transcription in human cells and to estimate their influence on protein coding expression patterns obtained by double-stranded microarrays, we profiled transcription with sense and antisense independently by using strand-specific cDNA microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4862

9 Samples

Download data

(Submitter supplied) Using RNA-seq, we report here that CodY regulation is hierarchically regulated in response to environmental starvation.

Organism:

Bacillus anthracis str. Sterne

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20947

24 Samples

Download data: TXT