Polony analysis of gene expression in ES cells and blastocysts

Nucleic Acids Research

Volumn 35, Issue 22, 2007, Pages

  Rieger, C ^a   Poppino, R ^a   Sheridan, R ^a   Moley, K ^a   Mitra, R ^a   Gottlieb, D ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GLUCOSE TRANSPORTER 1; MESSENGER RNA; OCTAMER TRANSCRIPTION FACTOR 4; REX PROTEIN; REX PROTEIN 1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CDX2; TRANSCRIPTION FACTOR NANOG; UNCLASSIFIED DRUG; ORGANIC CATION TRANSPORTER; SOLUTE CARRIER FAMILY 22 (ORGANIC CATION TRANSPORTER), MEMBER 3;

ANIMAL CELL; ARTICLE; BLASTOCYST; CELL ASSAY; CELL COUNT; CELL POPULATION; CONTROLLED STUDY; DNA DETERMINATION; EMBRYO; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; STEM CELL; ANIMAL; CELL LINE; EMBRYONIC STEM CELL; EVALUATION; GENETICS; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION;

ANIMALS; BLASTOCYST; CELL LINE; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; MICE; ORGANIC CATION TRANSPORT PROTEINS; POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 38049009475     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1076     Document Type: Article

References (31)

1. Chiang,M.K. and Melton,D.A. (2003) Single-cell transcript analysis of pancreas development. Dev. Cell, 4, 383-393.
2. Tietjen,I., Rihel,J.M., Cao,Y., Koentges,G., Zakhary,L. and Dulac,C. (2003) Single-cell transcriptional analysis of neuronal progenitors. Neuron, 38, 161-175.
3. Hartmann,C.H. and Klein,C.A. (2006) Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic Acids Res., 34, e143.
4. Bengtsson,M., Stahlberg,A., Rorsman,P. and Kubista,M. (2005) Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res. 15, 1388-1392.
5. Tang,F., Hajkova,P., Barton,S.C., Lao,K. and Surani,M.A. (2006) MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res., 34, e9.
6. Chetverina,H.V., Samatov,T.R., Ugarov,V.I. and Chetverin,A.B. (2002) Molecular colony diagnostics: Detection and quantitation of viral nucleic acids by in-gel PCR. Biotechniques, 33, 150-152, 154, 156.
7. Mitra,R.D. and Church,G.M. (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res., 27, e34.
8. Zhu,J., Shendure,J., Mitra,R.D. and Church,G.M. (2003) Single molecule profiling of alternative pre-mRNA splicing. Science, 301, 836-838.
9. Mitra,R.D., Shendure,J., Olejnik,J., Edyta Krzymanska,O. and Church,G.M. (2003) Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem., 320, 55-65.
10. Kim,J.B., Porreca,G.J., Song,L., Greenway,S.C., Gorham,J.M., Church,G.M., Seidman,C.E. and Seidman,J.G. (2007) Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science, 316, 1481-1484.
11. Bain,G., Kitchens,D., Yao,M., Huettner,J.E. and Gottlieb,D.I. (1995) Embryonic stem cells express neuronal properties in vitro. Dev. Biol. 168, 342-357.
12. Bain,G., Yao,M., Huettner,J.E., Finley,M. and Gottlieb,D.I. (1998) Culturing Nerve Cells. MIT Press, Cambridge, MA.
13. Moley,K.H., Chi,M.M. and Mueckler,M.M. (1998) Maternal hyperglycemia alters glucose transport and utilization in mouse preimplantation embryos. Am. J. Physiol., 275, E38-E47.
14. Mikkilineni,V., Mitra,R.D., Merritt,J., DiTonno,J.R., Church,G.M., Ogunnaike,B. and Edwards,J.S. (2004) Digital quantitative measurements of gene expression. Biotechnol. Bioeng., 86, 117-124.
15. Lee,T.I., Jenner,R.G., Boyer,L.A., Guenther,M.G., Levine,S.S., Kumar,R.M., Chevalier,B., Johnstone,S.E., Cole,M.F. et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell, 125, 301-313.
16. Boyer,L.A., Plath,K., Zeitlinger,J., Brambink,T., Medeiros,L.A., Lee,T.I., Levine,S.S., Wernig,M., Tajonar,A. et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature, 441, 349-353.
17. Pesce,M. and Scholer,H.R. (2001) Oct-4: Gatekeeper in the beginnings of mammalian development. Stem Cells, 19, 271-278.
18. Chisholm,J.C., Johnson,M.H., Warren,P.D., Fleming,T.P. and Pickering,S.J. (1985) Developmental variability within and between mouse expanding blastocysts and their ICMs. J. Embryol. Exp. Morphol., 86, 311-336.
19. Johnson,M.H. and McConnell,J.M. (2004) Lineage allocation and cell polarity during mouse embryogenesis. Semin. Cell Dev. Biol., 15 583-597.
20. Strumpf,D., Mao,C.A., Yamanaka,Y., Ralston,A., Chawengsaksophak,K., Beck,F. and Rossant,J. (2005) Cdx2 required for trophectoderm. Oct4 restricted to ICM. Development, 132, 2093-2102.
21. Carayannopoulos,M.O., Schlein,A., Wyman,A., Chi,M., Keembiyehetty,C. and Moley,K.H. (2004) GLUT9 is differentially expressed and targeted in the preimplantation embryo. Endocrinology, 145, 1435-1443.
22. Riley,J.K., Heeley,J.M., Wyman,A.H., Schlichting,E.L. and Moley,K.H. (2004) TRAIL and KILLER are expressed and induce apoptosis in the murine preimplantation embryo. Biol. Reprod., 71, 871-877.
23. Zhang,J., Tam,W.L., Tong,G.Q., Wu,Q., Chan,H.Y., Soh,B.S., Lou,Y., Yang,J., Ma,Y. et al. (2006) Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nat. Cell Biol., 8, 1114-1123.
24. Mitsui,K., Tokuzawa,Y., Itoh,H., Segawa,K., Murakami,M., Takahashi,K., Maruyama,M., Maeda,M. and Yamanaka,S. (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell, 113, 631-642.
25. Rogers,M.B., Hosler,B.A. and Gudas,L.J. (1991) Specific expression of a retinoic acid-regulated, zinc-finger gene, Rex-1, in preimplantation embryos, trophoblast and spermatocytes. Development, 113, 815-824.
26. Deb,K., Sivaguru,M., Yong,H.Y. and Roberts,R.M. (2006) Cdx2 gene expression and trophectoderm lineage specification in mouse embryos. Science, 311, 992-996.
27. Heilig,C.W., Saunders,T., Brosius,F.C. III, Moley,K., Heilig,K., Baggs,R., Guo,L. and Conner,D. (2003) Glucose transporter-1-deficient mice exhibit impaired development and deformities that are similar to diabetic embryopathy. Proc. Natl Acad. Sci. USA, 100, 15613-15618.
28. Zentilin,L. and Giacca,M. (2007) Competitive PCR for precise nucleic acid quantification. Nat. Protoc., 2, 2092-2104.
29. Dufva,M., Svenningsson,A. and Hansson,G.K. (1995) Differential regulation of macrophage scavenger receptor isoforms: MRNA quantification using the polymerase chain reaction. J. Lipid Res., 36, 2282-2290.
30. Warren,L., Bryder,D., Weissman,I.L. and Quake,S.R. (2006) Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc. Natl Acad. Sci. USA, 103, 17807-17812.
31. Mitra,R.D., Butty,V.L., Shendure,J., Williams,B.R., Housman,D.E. and Church,G.M. (2003) Digital genotyping and haplotyping with polymerase colonies. Proc. Natl Acad. Sci. USA, 100, 5926-5931.