title: Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing.
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 10(7) 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, approximately 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.
authors.affiliation: Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1066 Epalinges, Switzerland. Victor.Jongeneel@licr.ch
authors.forename: C Victor
authors.initials: CV
authors.lastname: Jongeneel
authors.forename: Christian
authors.initials: C
authors.lastname: Iseli
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Stevenson
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Riggins
authors.forename: Anita
authors.initials: A
authors.lastname: Lal
authors.forename: Alan
authors.initials: A
authors.lastname: Mackay
authors.forename: Robert A
authors.initials: RA
authors.lastname: Harris
authors.forename: Michael J
authors.initials: MJ
authors.lastname: O'Hare
authors.forename: A Munro
authors.initials: AM
authors.lastname: Neville
authors.forename: Andrew J G
authors.initials: AJ
authors.lastname: Simpson
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics; D001940:Breast / Q000378:metabolism; D002460:Cell Line; D003110:Colonic Neoplasms / Q000235:genetics; D004848:Epithelium / Q000378:metabolism; D020224:Expressed Sequence Tags; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D012333:RNA, Messenger