title: Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.
abstract: Despite the recent advance of single-cell gene expression analyses, co-measurement of both genomic and transcriptional signatures at the single-cell level has not been realized. However such analysis is necessary in order to accurately delineate how genetic information is transcribed, expressed, and regulated to give rise to an enormously diverse range of cell phenotypes. Here we report on a microfluidics-facilitated approach that allows for controlled separation of cytoplasmic and nuclear contents of a single cell followed by on-chip amplification of genomic DNA and cytoplasmic mRNA. When coupled with off-chip polymerase chain reaction, gel electrophoresis and Sanger sequencing, a panel of genes and transcripts from the same single cell can be co-detected and sequenced. This platform is potentially an enabling tool to permit multiple genomic measurements performed on the same single cells and opens new opportunities to tackle a range of fundamental biology questions including non-genetic cell-to-cell variability, epigenetic regulation, and stem cell fate control. It also helps address clinical challenges such as diagnosing intra-tumor heterogeneity and dissecting complex cellular immune responses.
authors.affiliation: 1] Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA [2].
authors.forename: Lin
authors.initials: L
authors.lastname: Han
authors.affiliation: 1] Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA [2] Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA [3] Department of Cell Biology, Second Military Medical University, Shanghai 200433, China [4].
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Zi
authors.affiliation: Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813 USA.
authors.forename: Lana X
authors.initials: LX
authors.lastname: Garmire
authors.affiliation: Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wu
authors.affiliation: 1] Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA [2] Yale Comprehensive Cancer Center, New Haven, CT 06520, USA.
authors.forename: Sherman M
authors.initials: SM
authors.lastname: Weissman
authors.affiliation: Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Pan
authors.affiliation: 1] Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA [2] Yale Comprehensive Cancer Center, New Haven, CT 06520, USA.
authors.forename: Rong
authors.initials: R
authors.lastname: Fan
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000235:genetics; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics; D006801:Humans; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000235:genetics* / Q000473:pathology; D044085:Microfluidics; D012333:RNA, Messenger / Q000096:biosynthesis; D059010:Single-Cell Analysis
chemical_list: D012333:RNA, Messenger; D004247:DNA