GEO DataSets

(Submitter supplied) We compared the gene expression profiles of prostate carcinoma cells, LNCaP, treated or not with an inhibitor of RNA Polymerase II (RNAP II), alpha-amanitin. These experiments pointed to a fraction of intronic messages that seems to be insensitive to alpha-amanitin or up-regulated in cells with blocked RNAP II transcription. Keywords: RNA-polymerase II inhibition experiments

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4051

8 Samples

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(Submitter supplied) The experiments described here aim to generate a set of gene expression profiles from prostate, liver and kidney tissues using a custom-designed oligo-array platform enriched in messages that map to intronic regions of known human genes. Expression profiles of these tissues were combined in order to find a tissue-specific signature of intronic transcripts. Keywords: Tissue-specific, Intronic transcripts

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4051

12 Samples

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(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (ncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

38 Samples

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(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:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

36 Samples

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(Submitter supplied) Transcriptional profiling of HeLa cells treated with α-amanitin for 9 h. Relative abundance to untreated control cells was used to evaluate the biogenesis of lncRNAs by RNA polymerase II.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) HeLa cells were fractioned in nucleus and cytoplasm to investigate the subcellular distribution of lncRNAs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

2 Samples

Download data: TXT

(Submitter supplied) RNA aliquots were digested with 5’-phosphate-dependent exonuclease (5'-exo) following pre-treatment with tobacco acid pyrophosphatase (TAP) to release the 5’ cap and render the RNA susceptible to 5’ exonuclease digestion (TAP+/5'-exo+). Two color array hybridizations were performed and TAP+/5'-exo+ samples were compared with TAP-/5'-exo+ control samples.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of HeLa cells treated with actinomycin D for increasing amounts of time. Relative abundance to control cells was used to estimate the half-life of lncRNAs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

20 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Mia PaCa 2 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of MCF-7 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of DU-145 cells treated with 5-Aza for 72 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

58 Samples

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(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4051 GPL3985

80 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL4051

4 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3985

32 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3985

44 Samples

Download data: TXT

(Submitter supplied) The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from 6 patients. A custom-built cDNA microarray platform was used, comprising 2,292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

48 Samples

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

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

20 Samples

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(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

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(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

17 Samples

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