publication_authors:Joab I Results

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Microarray (72)

Rna-seq (12)

Platform

Affymetrix Mouse Gene 2.1 ST Array (mogene21st) (40)

Illumina HiSeq 2000 (40)

Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2) (20)

Illumina HiSeq 2000 (12)

Affymetrix Human Genome U133A 2.0 Array (hgu133a2) (12)

Includes Publication (12)

GSE34573

A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels

Homo sapiens
20 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Previous studies have reported that the tumour cells of nasopharyngeal carcinoma (NPC) exhibit both recurrent chromosome abnormalities and changes in the expression of numerous genes. However, it is not known to what extent changes in the copy number of individual genes are associated with the observed expression changes. To address this, a genome wide analysis of chromosome copy number and gene expression was performed in tumour cells micro-dissected from the same NPC biopsies. Significant gene expression changes were identified in tumour suppressor genes (TSGs) and in tumour-promoting genes (TPGs) but almost 60% of these can be either upregulated or downregulated in different types of cancer. This suggests that the simplistic classification of genes as TSGs or TPGs may not be entirely appropriate and that the concept of onco-suppressors may be more extensive than previously recognised. Several genomic regions showing frequent copy number gain or loss were identified. Whereas TSGs were significantly enriched within regions of frequent loss, no significant enrichment of TPGs was observed in regions of frequent gain. However, on a gene by gene basis little correlation was found between DNA copy number and alterations in gene expression except for loss of expression from homozygous deletions and a single highly amplified segment which showed enhanced gene expression.

Publication Title

A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels.

Sample Metadata Fields

Disease, Disease stage

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SRP059912

Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting

Glycine max
12 Downloadable Samples
Illumina HiSeq 2000

Description

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition Overall design: Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and sequenced on an Illumina Hi-Seq 2000 platform. The RNA concentration of each sample was approximately 200ng/µl with a quantity of 50 µl.isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays