GEO DataSets

(Submitter supplied) Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH). Keywords: Repeat sample.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2920

68 Samples

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(Submitter supplied) Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.

Organism:

Homo sapiens

1 Series

68 Samples

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(Submitter supplied) Introduction: Human Papilloma Virus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC), between 15% and 35% of HNSCC harboring HPV, almost exclusively of subtype 16. Demographic and exposure differences between HPV-positive (+) and negative (-) HNSCCs suggest that HPV(+) tumors may constitute a subclass with different biology, while clinical differences have also been observed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1667

Platform:

GPL570

36 Samples

Download data: CEL

Analysis of 8 head and neck squamous cell carcinoma (HNSCC) tumors positive for human papilloma virus (HPV). 28 HNSCC HPV negative tumors examined. Between 15% and 35% of HNSCCs harbor HPV DNA. Results provide insight into the effect of HPV infection in HNSCC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 infection sets

Platform:

GPL570

Series:

GSE3292

36 Samples

Download data: CEL

(Submitter supplied) Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides. Keywords = Matrix-CGH Keywords = array-CGH

Organism:

Homo sapiens

1 Series

94 Samples

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(Submitter supplied) We sought to apply the technologies of gene expression profiling to detect genes significant in the aetiology of cervical carcinoma . We investigated 14 normal (NAD), 11 low grade squamous intrapepithelial lesions (LSIL), 21 high grade squamous intraepithelial lesions (HSIL) and 28 squamous cell carcinomas by Affymetrix GeneChip whole transcriptome profiling. Two SCC cell lines were also included in the cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL571

77 Samples

Download data: CEL

(Submitter supplied) Detection of copy number dependent gene expression profiles in epithelial tumours has lead to the discovery of genes significant in diagnosis, prognosis and of therapeutic value. We sought to apply the technologies of gene expression profiling and copy number aberration detection by high density oligonucleotide microarray analysis to detect genes with expression profiles regulated by copy number. We surveyed copy number aberrations in 27 squamous cell carcinomas tissues and ten cervical carcinoma cell lines by Agilent 244k aCGH, and in a companion study of 77 tissues we obtained transcriptional profiles of a broader ranger of histologies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9128

37 Samples

Download data: GPR, TXT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by array; Expression profiling by array

5 related Platforms

200 Samples

Download data: CEL, GPR

(Submitter supplied) For many oncogenes, increased expression resulting from copy number gain confers a selective advantage to cells that consequently make up the tumour bulk. To identify oncogenes of potential biological significance in cervical squamous cell carcinoma (SCC), 36 primary samples and ten cell lines were screened by array comparative genomic hybridization (CGH). The most commonly occurring regions of copy number gain that also showed amplification were 5p15.2–14.3 (59%), 5p13.3 (65%), and 5p13.2–13.1 (63%). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13177

40 Samples

Download data: GPR

(Submitter supplied) For many oncogenes, increased expression resulting from copy number gain confers a selective advantage to cells that consequently make up the tumour bulk. To identify oncogenes of potential biological significance in cervical squamous cell carcinoma (SCC), 36 primary samples and ten cell lines were screened by array comparative genomic hybridization (CGH). The most commonly occurring regions of copy number gain that also showed amplification were 5p15.2–14.3 (59%), 5p13.3 (65%), and 5p13.2–13.1 (63%). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13176

46 Samples

Download data: GPR, TXT

(Submitter supplied) Background: The high incidence of recurrence and unpredictable clinical outcome for paediatric ependymoma reflect the imprecision of current therapeutic staging and need for novel risk stratification markers. Gain of chromosome 1q has been reported as a frequent aberration and correlate of adverse outcome in ependymoma. We therefore evaluated a prognostic role for 1q25 gain across three age-defined European clinical trial cohorts of paediatric intracranial ependymoma. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL3718 GPL3720

182 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Ependymomas are glial tumors that share morphologic similarities with ependymal cells. Here we laser microdissected ependymoma cells of 15 infratentorial tumors and generated gene expression profiles. These profiles were compared to those of 7 laser microdissected ependymal tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

22 Samples

Download data: CEL

(Submitter supplied) This set contains the aCGH data for the publication. Previous low-resolution studies of chromosome 22 in ovarian carcinoma have suggested its involvement in the development of the disease. We report a high-resolution analysis of DNA copy number and gene expression of 22q in 18 ovarian carcinomas using a 22q-specific genomic microarray. We identified aberrations in 67% of the studied tumors, which displayed 3 distinct gene copy number profiles. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

5 related Platforms

15 Samples

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(Submitter supplied) Transcriptomic profiling of human breast tumors. Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 53 invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Array-CGH results was validated by FISH using tumors showing 8p11-p12 DNA amplification and expression profiling was confirmed using qPCR for 11 transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

53 Samples

Download data: IDAT, TXT

(Submitter supplied) Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL6947 GPL9077

194 Samples

Download data: CSV, GPR, IDAT

(Submitter supplied) Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9077

97 Samples

Download data: GPR

(Submitter supplied) Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

97 Samples

Download data: CSV, IDAT, TXT

(Submitter supplied) Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH). Tumor DNA was hybridized against a single standard reference DNA-pool of the opposite sex than the patient. Every experiment was performed as dye-swap. Keywords: repeat sample

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL1432

94 Samples

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(Submitter supplied) We compared the prognostic significance of ectodomain isoforms of the epidermal growth factor receptor (EGFR), which lack the tyrosine kinase (TK) domain, with that of the full length receptor and its autophosphorylation status in cervical cancers treated with conventional chemoradiotherapy. We further explored signaling pathways that were correlated with high expression of ectodomain isoforms by gene expression analysis of 110 of the tumors, and validated the results in an independent cohort of 41 tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

151 Samples

Download data: TXT

(Submitter supplied) Rhabdomyosarcoma (RMS) is the most common paediatric soft-tissue sarcoma and resembles developing skeletal muscle. Specific genomic alterations including translocations, deletions and amplification events have been associated with the alveolar and embryonal subtypes of RMS. Characterizing these changes has led to increased understanding of the underlying molecular biology. However, further aberrations and their significance remain to be defined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

13 Samples

Download data: CEL, CHP