Dataset features


Application: Gene expression microarray analysis
Number of samples: 6
Release date: Dec 30 2005
Last update date: Mar 16 2012
Access: Public
Diseases: Breast Neoplasms
Chemicals: Estrogens
Dataset link Cell type and culture condition-dependent alternative splicing in human breast cancer cells

Experimental Protocol

The design of oligonucleotides is for the general detection of splicing variants from a given gene. The junction oligonucleotides consist of exon?exon junction sequence, because different splice variants will have different exon?exon junctions. The microarray also contains oligonucleotides that are complementary to flanking constitutive exons, and the alternative exon. This splicing-sensitive microarray was used because a signal derived from the hybridization to the constitutive exon oligonucleotides would, in theory, reflect the total amount of RNA from the particular gene, whereas hybridization signals from an exon-exon junction oligonucleotide would reflect the amount of RNA containing that particular junction. The ratio of hybridization intensity from an oligonucleotide spanning a specific exon-exon junction to that from a constitutive exon oligonucleotide would provide information about the level of that alternatively spliced RNA in the two comparison samples. Using this type of splicingsensitive array, one can acquire two sets of information from one array: expression level changes for the gene and changes in the distribution of the splice variants. The array used in this study contained 64 genes that underwent alternative splicing, including estrogen receptor 1 and 2 (ER1 and ER2), CD44 (cell adhesion molecule), ITGA6 (integrin a6 precursor), FAS, LARD, WT1 (Wilm?s tumor protein 1), and TP73 (tumor suppressor p73). Each gene could contain one or more simple alternative exons, or more complex arrangements of multiple alternative exons.