GEO DataSets

(Submitter supplied) We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

92 Samples

Download data: CEL, CHP

(Submitter supplied) We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

15 Samples

Download data: CEL, CHP

(Submitter supplied) We analyzed, by last-generation high-resolution SNP arrays, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the number of tumor-associated copy number abnormalities (CNAs) and copy neutral-loss of heterozygosity (CN-LOH) regions per patient and to identify possible recurring genomic abnormalities.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

97 Samples

Download data: CEL, CNCHP

(Submitter supplied) Clinical Significance: Understanding the differences in colorectal cancer (CRC) aggressiveness and clinical outcomes in relation to tumor stage and different molecular subsets is at most important for designing treatment regimens. However, molecular signatures for specific phenotypic subsets that predict the aggressiveness and clinical outcomes of CRC, specifically in advanced disease stage are lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4384

Platform:

GPL570

10 Samples

Download data: CEL

Analysis of Stage III CRCs exhibiting microsatellite-stable (MSS) and mutant p53 phenotypic features. p53 mutations are associated with higher Stage III MSS CRC mortality than p53 wild-type phenotypes. Results provide further insight into the prognostic value of p53 mutations in Stage III MSS CRCs.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL570

Series:

GSE27157

10 Samples

Download data: CEL

(Submitter supplied) Samples were taken from colorectal cancers in surgically resected specimens in 155 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifier was applied to these samples. Keywords: Expression profiling by array

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

155 Samples

Download data: CEL, TXT

(Submitter supplied) Samples were taken from colorectal cancers in surgically resected specimens from 74 patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifer was applied to these samples. Keywords: Expression profiling by array

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

74 Samples

Download data: CEL

(Submitter supplied) As part of a genomic profiling study of CRCs with MSI, we have performed genome-wide expression analyses of a consecutive patient series.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

34 Samples

Download data: CEL, CHP

(Submitter supplied) We have performed genome-wide expression analyses as part of a multi-omics study on 34 colorectal cancer cell lines. The data were used for gene expression subtyping of cell lines, gene set analyses and integration with DNA and protein level data.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

34 Samples

Download data: CEL, CHP

(Submitter supplied) Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Sco1 is a gene required for cytochrome c oxidase biogenesis and the regulation of copper homeostasis. We characterized the transcriptional changes that occur as a result of liver-specific deletion of Sco1 in mice at 27 days of age In this dataset, we include the expression data obtained from dissected wild-type mouse livers and mouse livers in which Sco1 has been specifically deleted.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

8 Samples

Download data: CEL

(Submitter supplied) The specific genes that influence neuroblastoma biology and are targeted by genomic alterations remain largely unknown. We quantified mRNA expression in a highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors and the expression profiles were determined using Affymetrix U95Av2 arrays. Comparisons between the sample groups allow the identification of genes with localized expression patterns. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

102 Samples

Download data: CEL

(Submitter supplied) We analysed the transcriptome profile by RNA-seq when knockdown ZIP7 by two individual siRNAs in MDAMB231 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10123 GPL15182

172 Samples

Download data: TXT

(Submitter supplied) The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL15182

88 Samples

Download data: TXT

(Submitter supplied) The concept of the CpG island methylator phenotype (CIMP) in colorectal cancers (CRCs) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects early during carcinogenesis remains largely unknown. Our aim was to uncover the molecular evolution of CIMP CRCs through integrative analysis of endoscopic, histological and molecular signatures in precancerous and malignant colorectal lesions.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10123

84 Samples

Download data: TXT

(Submitter supplied) We investigate different types of non-co-linear RNA, for example, circular, trans-splicing and gene fusion.

Organism:

Homo sapiens; Macaca mulatta

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL24106 GPL21454 GPL16791

17 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL1266 GPL96 GPL2641

88 Samples

Download data: CEL

(Submitter supplied) This study used tumour and paired normal samples from 28 Sézary Syndrome (SS) patients to define recurrent regions of chromosomal aberrations. Our data identified recurrent losses of 17p13.2-p11.2 and 10p12.1-q26.3 occurring in 71 and 68% of cases respectively; common gains were detected for 17p11.2-q25.3 (64%) and chromosome 8/8q (50%). Moreover, we identified novel genomic lesions recurring in more than 30% of tumours: loss of 9q13-q21.33 and gain of 10p15.3-10p12.2. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

32 Samples

Download data: CEL

(Submitter supplied) This study used tumour and paired normal samples from 28 Sézary Syndrome (SS) patients to define recurrent regions of chromosomal aberrations. Our data identified recurrent losses of 17p13.2-p11.2 and 10p12.1-q26.3 occurring in 71 and 68% of cases respectively; common gains were detected for 17p11.2-q25.3 (64%) and chromosome 8/8q (50%). Moreover, we identified novel genomic lesions recurring in more than 30% of tumours: loss of 9q13-q21.33 and gain of 10p15.3-10p12.2. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL1266 GPL2641

56 Samples

Download data: CEL