Analyzing Prostate Cancer Cell Line Transcriptome
Author Information
Author(s): Matthew N Bainbridge, René L Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, Anne Go, Allen Delaney, Malachi Griffith, Matthew Hickenbotham, Vincent Magrini, Elaine R Mardis, Marianne D Sadar, Asim S Siddiqui, Marco A Marra, Steven J Jones
Primary Institution: British Columbia Cancer Agency (BCCA) Genome Sciences Centre
Hypothesis
Using sequencing-by-synthesis will provide a quantitative measure of transcript abundance and identify splice variants in the LNCaP prostate cancer cell line.
Conclusion
High-throughput sequencing-by-synthesis methods can effectively profile the transcriptome, revealing many transcripts and novel splicing events in prostate cancer cells.
Supporting Evidence
- The study generated approximately 20 megabases of EST data.
- Transcription was detected from over 10,000 gene loci.
- 25 previously undescribed alternative splicing events were identified.
- Over 1,500 high-quality single nucleotide discrepancies were found.
Takeaway
Scientists used a special method to read the genes in prostate cancer cells, finding many important gene messages and some new ways those messages can be put together.
Methodology
Massively parallel sequencing-by-synthesis was used to generate expressed sequence tags (ESTs) from the LNCaP cell line treated with synthetic androgen R1881.
Potential Biases
Potential biases from bacterial host-associated cloning and sequencing errors.
Limitations
The study may have biases due to the sequencing method and the nature of the cell line used.
Participant Demographics
LNCaP human prostate cancer cell line.
Statistical Information
P-Value
p ≤ 9 × 10-7
Statistical Significance
p ≤ 0.05
Digital Object Identifier (DOI)
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