ALEXA-Seq

ALEXA-Seq analyzes massively parallel RNA sequencing data to catalog transcripts and evaluate differential and alternative expression patterns of known and predicted mRNA isoforms across cells and tissues.

Key Features:

• Massively Parallel Sequencing: Processes RNA-seq data generated by massively parallel RNA sequencing to profile transcriptomes.
• Cataloging Transcripts: Catalogs known and predicted transcripts to provide a detailed mRNA isoform landscape within samples.
• Assessment of Differential and Alternative Expression: Detects differential expression and alternative splicing events, including exon skipping, alternative splice site usage, and intron retention.
• Validation Methods: Supports validation of findings using reverse transcription-PCR (RT-PCR), quantitative PCR (qPCR), and Sanger sequencing.
• Comparative Analysis: Benchmarks results against exon tiling and splicing microarrays to assess sensitivity and specificity for alternative expression detection.
• Database Integration: Integrates alternative expression annotation databases to enhance interpretation of sequencing results.

Scientific Applications:

• Comparative cancer cell line analysis: Applied to fluorouracil-resistant versus nonresistant human colorectal cancer cell lines to detect global disruptions in splicing patterns and emergence of novel mRNA isoforms.
• Alternative splicing and expression studies: Used to explore transcriptome complexity by identifying alternative splicing and differential expression across biological contexts.

Methodology:

Processing and analysis of RNA sequencing data to identify and quantify transcript variants; detection of novel splicing events including exon skipping, alternative splice site usage, and intron retention; and integration with alternative expression annotation databases.