GEO DataSets

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array

Platform:

GPL7822

252 Samples

Download data: GPR

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

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platforms:

GPL7821 GPL7822

295 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platform:

GPL7821

43 Samples

Download data

(Submitter supplied) Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain. Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations. more...

Organism:

Mus musculus

Type:

Expression profiling by array

5 related Platforms

7 Samples

Download data: CEL

(Submitter supplied) Expression of the sense-antisense transcripts (SATs). Methods: The sequences of 60mer DNA specific to the sense and antisense genes were chosen by K.K. DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information. RNA was labeled and hybridized using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer's protocols. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1819

10 Samples

Download data

(Submitter supplied) The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. more...

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by genome tiling array

27 related Platforms

27 Samples

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(Submitter supplied) Recent high-throughput transcriptome analyses have revealed that >90% of all human DNA is transcribed. The vast majority of these transcripts are non-coding, thus challenging the classical definition of what constitutes a gene and, by association, a promoter. Adding to the complexity, short-lived transcripts have likely gone unnoticed. Here, we couple RNAi-depletion of one of the major RNA degradation activities, the human 3’-5’ exoribonucleolytic exosome with ENCODE microarrays tiling 1% of the human genome, to reveal a new class of short, polyadenylated and highly unstable transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL7161

1 Sample

Download data: TXT

(Submitter supplied) The objective of the study is to obtain a high resolution transcription map of S. pneumoniae genome and make it available through a genome browser. The study also help to identify gene expression pattern, presence of small RNAs, Antisense expression and operon structure.

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by genome tiling array

Platform:

GPL7177

2 Samples

Download data: PAIR

(Submitter supplied) It has been postulated that noncoding RNAs (ncRNAs) are involved in the post-transcriptional control of gene expression, and may have contributed to the emergence of the complex attributes observed in mammalians. The complement of ncRNAs expressed from intronic regions of the human and mouse genomes comprises at least 78,147 and 39,660 transcriptional units, respectively. To identify conserved intronic sequences expressed in both humans and mice, we used custom-designed human cDNA microarrays to separately interrogate RNA from mouse and human liver, kidney and prostate tissues. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platform:

GPL3985

36 Samples

Download data

(Submitter supplied) To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17884

26 Samples

Download data: TXT, WIG

(Submitter supplied) Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.

Organism:

Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13168

6 Samples

Download data: PAIR

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

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL8486 GPL13168

12 Samples

Download data: PAIR

(Submitter supplied) Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL13168 GPL8486

12 Samples

Download data: PAIR

(Submitter supplied) Genomic DNA prepared from B. subtilis 168 cells grown to stationary phase was hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347).

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Other

Platform:

GPL13168

4 Samples

Download data: PAIR

(Submitter supplied) This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis

Type:

Expression profiling by genome tiling array

Platform:

GPL13168

6 Samples

Download data: PAIR

(Submitter supplied) Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an excellent coverage of the transcriptome of this bacterium. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL13149

269 Samples

Download data: PAIR

(Submitter supplied) Increasing numbers of sense–antisense transcripts (SATs), which are transcribed from the same chromosomal location but in opposite directions, have been identified in various eukaryotic species, but the biological meanings of most SATs remain unclear. To improve understanding of natural sense–antisense transcription, we performed comparative expression profiling of SATs conserved among humans and mice. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6120 GPL6119

20 Samples

Download data

(Submitter supplied) High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of Porphyromonas gingivalis. The compiled P. gingivalis transcriptome were based on total RNA samples isolated from three different laboratory culturing conditions and the strand-specific transcription profiles generated covered the entire genome including both protein coding and non-coding regions. more...

Organism:

Porphyromonas gingivalis W83

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13827

3 Samples

Download data: TXT

(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 innocua Clip11262; Listeria monocytogenes EGD-e

Type:

Other

Platforms:

GPL15272 GPL15273

16 Samples

Download data: TXT

(Submitter supplied) In this study, we investigated the transcriptional response of the human isolate L. reuteri ATCC 55730 during sourdough fermentation by using whole-genome microarrays. Significant changes of mRNA levels were found for 101 genes involved in diverse cellular processes, e.g., carbohydrate and energy metabolism, cell envelope biosynthesis, exopolysaccharide production, stress responses, signal transduction and cobalamin biosynthesis. more...

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL6366

6 Samples

Download data: GPR