Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing
- C. Victor Jongeneel*,†,
- Christian Iseli*,
- Brian J. Stevenson*,
- Gregory J. Riggins‡,
- Anita Lal‡,
- Alan Mackay§,
- Robert A. Harris§,
- Michael J. O'Hare§,
- A. Munro Neville¶,
- Andrew J. G. Simpson¶, and
- Robert L. Strausberg‖
- *Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1066 Epalinges, Switzerland; ¶Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10012; ‖Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892; §Ludwig Institute for Cancer Research, London UCL Branch, London W1W 7BS, United Kingdom; and ‡Department of Pathology, Duke University Medical School, Durham, NC 27710
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Communicated by Webster K. Cavenee, University of California at San Diego, La Jolla, CA (received for review January 29, 2003)
Abstract
Whereas information is rapidly accumulating about the structure and position of genes encoded in the human genome, less is known about the complexity and relative abundance of their expression in individual human cells and tissues. Here, we describe the characteristics of the transcriptomes of two cultured cell lines, HB4a (normal breast epithelium) and HCT-116 (colon adenocarcinoma), using massively parallel signature sequencing (MPSS). We generated in excess of 107 short signature sequences per cell line, thus providing a comprehensive snapshot of gene expression, within the technical limitations of the method. The number of genes expressed at one copy per cell or more in either of the lines was estimated to be between 10,000 and 15,000. The vast majority of the transcripts found in these cells can be mapped to known genes and their polyadenylation variants. Among the genes that could be identified from their signature sequences, ≈8,500 were expressed by both cell lines, whereas 6,000 showed cellular specificity. Taking into account sequence tags that map uniquely to the genome but not to known transcripts, overall the data are consistent with an upper limit of 17,000 for the total number of genes expressed at more than one copy per cell in one or both of the two cell lines examined.
Footnotes
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↵ † To whom correspondence should be addressed at: Office of Information Technology, Ludwig Institute for Cancer Research, 155 Chemin des Boveresses, CH-1066 Epalinges, Switzerland. E-mail: Victor.Jongeneel{at}licr.org.
- Abbreviations:
- MPSS,
- massively parallel signature sequencing;
- tpm,
- tags per million;
- SAGE,
- serial analysis of gene expression
- Copyright © 2003, The National Academy of Sciences
