title: Highly parallel genome-wide expression analysis of single mammalian cells.
abstract: BACKGROUND
  We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs.
  
  
  RESULTS
  The method uses tagged priming and template-switching, resulting in the incorporation of universal PCR priming sites at both ends of the synthesized cDNA for global PCR amplification. Coupled with a whole-genome gene expression microarray platform, we routinely obtain expression correlation values of R(2)~0.76-0.80 between individual cells and R(2)~0.69 between 50 pg total RNA replicates. Expression profiles generated from single cells or 50 pg total RNA correlate well with that generated with higher input (1 ng total RNA) (R(2)~0.80). Also, the assay is sufficiently sensitive to detect, in a single cell, approximately 63% of the number of genes detected with 1 ng input, with approximately 97% of the genes detected in the single-cell input also detected in the higher input.
  
  
  CONCLUSIONS
  In summary, our method facilitates whole-genome gene expression profiling in contexts where starting material is extremely limiting, particularly in areas such as the study of progenitor cells in early development and tumor stem cell biology.
authors.affiliation: Research and Development, Illumina, Inc, San Diego, California, United States of America. jfan@illumina.com
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.forename: Craig S
authors.initials: CS
authors.lastname: April
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Fisher
authors.forename: Brandy
authors.initials: B
authors.lastname: Klotzle
authors.forename: Marina
authors.initials: M
authors.lastname: Bibikova
authors.forename: Fiona
authors.initials: F
authors.lastname: Kaper
authors.forename: Mostafa
authors.initials: M
authors.lastname: Ronaghi
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
authors.forename: Takayo
authors.initials: T
authors.lastname: Ota
authors.forename: Jeremy
authors.initials: J
authors.lastname: Chien
authors.forename: Louise C
authors.initials: LC
authors.lastname: Laurent
authors.forename: Jeanne F
authors.initials: JF
authors.lastname: Loring
authors.forename: Sean V
authors.initials: SV
authors.lastname: Nisperos
authors.forename: Gina Y
authors.initials: GY
authors.lastname: Chen
authors.forename: Jiang F
authors.initials: JF
authors.lastname: Zhong
mesh_terms: D000818:Animals; D002477:Cells; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods