GEO DataSets

(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:

GPL10637 GPL10636

12 Samples

Download data: TXT

(Submitter supplied) It has previously been shown that Isw2 represses cryptic antisense transcripts from the 3’-end of three genes. However, whether Isw2 generally functions to repress cryptic RNA transcription is currently unknown. We thus sought to determine the loci at which Isw2 is required to repress cryptic non-coding RNA (ncRNA) expression and to map their transcription start sites relative to nucleosome positions on a global scale.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by genome tiling array

Platform:

GPL10725

21 Samples

Download data: PAIR

(Submitter supplied) We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors 1 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3292

35 Samples

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(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

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(Submitter supplied) Invasion of host tissue by the human fungal pathogen, Candida albicans is an important step during many forms of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. It is known for example that the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade into host tissue and to cause infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence as compared to SC5314. more...

Organism:

Candida albicans

Type:

Genome variation profiling by array

Platform:

GPL6453

2 Samples

Download data: GPR

(Submitter supplied) Genome-wide detection of novel non-coding RNAs in S. cerevisiae by modulating an RNase P pathway through the depletion of a component RPP1. Keywords: time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL3471

8 Samples

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(Submitter supplied) GenBank accession numbers: NC_001133-NC_001148, NC_001224 Protocol: Maskless Array Synthesizer (MAS)

Organism:

Saccharomyces cerevisiae

1 Series

8 Samples

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(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) Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9854

31 Samples

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) Survey of transcriptional activity across 22.6% of the P. falciparum strain 3D7 genome. 872 protein coding genes and 60 putative P. falciparum lncRNAs identified under developmental regulation during the parasite's pathogenic human blood stage.

Organism:

Plasmodium falciparum 3D7; Plasmodium falciparum

Type:

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

Platform:

GPL13278

4 Samples

Download data: GFF

(Submitter supplied) The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. more...

Organism:

Histoplasma capsulatum

Type:

Expression profiling by genome tiling array

93 related Platforms

93 Samples

Download data: GPR

(Submitter supplied) Deep sequencing of mRNA from six different tissues

Organism:

Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16440

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) The transcriptional changes in Escherichia coli upon induction of the SOS response are investigated by utilizing custom designed oligonucleotide microarrays. Keywords: Gene expression during the SOS response in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL7714

10 Samples

Download data: CEL

(Submitter supplied) The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq in which cDNA fragments are subjected to high throughput sequencing. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genomeand demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL6750

1 Sample

Download data: TXT

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

Organism:

Candida parapsilosis

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13192 GPL14718

34 Samples

Download data: GPR, SAM

(Submitter supplied) We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations.

Organism:

Candida parapsilosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14718

26 Samples

Download data: SAM

(Submitter supplied) Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis UPC2 delete in hypoxia.

Organism:

Candida parapsilosis

Type:

Expression profiling by array

Platform:

GPL13192

4 Samples

Download data: GPR

(Submitter supplied) Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition.

Organism:

Candida parapsilosis

Type:

Expression profiling by array

Platform:

GPL13192

4 Samples

Download data: GPR

(Submitter supplied) Identification of novel transcribed sequences in Arabidopsis thaliana using high density genome tiling arrays. Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

13 related Platforms

13 Samples

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