GEO DataSets

(Submitter supplied) Reporters were arranged in 12 sub-arrays containing each one 12 rows and 32 columns of spots (384 spots/sub-array). Rows 1 to 5 comprise nomatch human cDNAs. Rows 6 to 10 comprise cDNAs from known human genes. Rows 11 and 12 of each sub-array contain the 32 ScoreCard control cDNAs and 32 prostate expressed control cDNAs plus housekeeping cDNAs, respectively. Protocol: The microarray platform used in this project deploys up to 4,608 distinct cDNA spots in duplicate per glass slide, comprising a total of 9,216 elements per array. more...

Organism:

Homo sapiens

7 Series

256 Samples

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(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) 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) 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) 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) To better understand the molecular mechanism that underlay tumorigenesis and progression of prostate cancer (PCa), we studied the gene expression profiles of sixteen PCa compared to their matched normal tissues. Using Significance Analysis of Microarrays, we identified 53 genes differentially expressed that were more than 2 fold up- or down-regulated in at least 50 % of the tumors. Keywords: disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1998

16 Samples

Download data: GPR

(Submitter supplied) Patients with high-risk localized prostate cancer (tumor-node-metastasis ≥ T2b or prostate-specific antigen ≥ 15 ng/mL or Gleason glade ≥ 4+3) were enrolled into a phase II clinical trial of neoadjuvant chemotherapy with docetaxel and mitoxantrone followed by prostatectomy. Pretreatment prostate tissue was acquired by needle biopsy and posttreatment tissue was acquired by prostatectomy. Prostate epithelium was captured by microdissection, and transcript levels were quantitated by cDNA microarray hybridization.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4767 GPL4763

31 Samples

Download data: TXT

(Submitter supplied) The histopathological and molecular heterogeneity of prostate cancer and the limited availability of human tumor tissue make unraveling the mechanisms of prostate carcinogenesis a challenging task. Our goal was to develop an ex vivo model that could be reliably utilized to define a prognostic signature based on gene expression profiling of cell cultures that maintained the tumor phenotype. To this end, we derived epithelial cultures from tissue explanted from 59 patients undergoing radical prostatectomy or cistoprostatectomy because of Prostate Benign Hyperplasia/Prostate Cancer or Bladder Carcinoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1746

Platform:

GPL96

30 Samples

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Analysis of epithelial cell cultures from prostate tumor explants. Results identify an epithelial-restricted transcription profile that can be integrated with tumor grade and clinical information with the aim of discriminating indolent and aggressive prostate tumors that are histologically similar.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 7 disease state, 2 protocol sets

Platform:

GPL96

Series:

GSE3868

30 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) 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

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(Submitter supplied) Laryngeal squamous cell carcinoma is a very common in head and neck cancer, accounting for 25% of all cases, with high mortality rates and poor prognosis. In this study, we compared expression profiles of clinical samples from15 larynx tumors and 10 non-neoplastic larynx tissue using a custom-built cDNA microarray containing 332 probes for 285 genes previously identified as up- or down-regulated in head and neck tumors by the Head and Neck Annotation Consortium (Reis et al., Cancer Res 65:1693-99, 2005). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6426

46 Samples

Download data: TXT

(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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