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Alternative expression analysis by RNA sequencing
- Source :
- Nature Methods. 7:843-847
- Publication Year :
- 2010
- Publisher :
- Springer Science and Business Media LLC, 2010.
-
Abstract
- In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. As proof of principle, we used the approach to compare fluorouracil-resistant and -nonresistant human colorectal cancer cell lines. We assessed the sensitivity and specificity of the approach by comparison to exon tiling and splicing microarrays and validated the results with reverse transcription-PCR, quantitative PCR and Sanger sequencing. We observed global disruption of splicing in fluorouracil-resistant cells characterized by expression of new mRNA isoforms resulting from exon skipping, alternative splice site usage and intron retention. Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at http://www.alexaplatform.org/alexa_seq/.
- Subjects :
- Gene isoform
Antimetabolites, Antineoplastic
genetic processes
Gene Expression
Biology
Biochemistry
Cell Line, Tumor
Databases, Genetic
Expression analysis
Humans
Protein Isoforms
natural sciences
RNA, Messenger
Molecular Biology
Oligonucleotide Array Sequence Analysis
Sequence (medicine)
Expressed Sequence Tags
Genetics
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, RNA
Gene Expression Profiling
RNA
Cell Biology
Alternative Splicing
Drug Resistance, Neoplasm
Fluorouracil
Colorectal Neoplasms
Sequence Alignment
Biotechnology
Subjects
Details
- ISSN :
- 15487105 and 15487091
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- Nature Methods
- Accession number :
- edsair.doi.dedup.....a2cf34ad6a62f79474a35b8038a4ca3a