Whole genome amplification by T7-based linear amplification of DNA (TLAD): Overview

Cold Spring Harbor Protocols

Volumn 3, Issue 5, 2008, Pages

  Liu, Chih Long ^a   Bernstein, Bradley E ^a   Schreiber, Stuart L ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA NUCLEOTIDYLEXOTRANSFERASE; DOUBLE STRANDED DNA; GENOMIC DNA; RNA POLYMERASE;

BACTERIOPHAGE T7; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA DETERMINATION; DNA FRAGMENTATION; DNA MICROARRAY; DNA TEMPLATE; GENE AMPLIFICATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOME SIZE; IN VITRO STUDY; METHODOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; REVIEW; SACCHAROMYCES CEREVISIAE;

EID: 55249096909     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top42     Document Type: Review

References (18)

1. Baugh, L.R., Hill, A.A., Brown, E.L., and Hunter, C.P. 2001. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29: e29. doi: 10.1093/nar/29.5.e29.
2. Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O., and Schreiber, S.L. 2004. Global nucleosome occupancy in yeast. Genome Biol. 5: R62. doi: 10.1186/gb-2004-5-9-r62.
3. Bernstein, B.E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas III, E.J., Gingeras, T.R., et al. 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169-181.
4. Bohlander, S.K., Espinosa III, R., Le Beau, M.M., Rowley, J.D., and Diaz, M.O. 1992. A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics 13: 1322-1324.
5. Buck, M.J. and Lieb, J.D. 2004. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349-360.
6. Gerton, J.L., DeRisi, J., Shroff, R., Lichten, M., Brown, P.O., and Petes, T.D. 2000. Inaugural article: Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 97: 11383-11390.
7. Humphrey, E.L., Shamji, A.F., Bernstein, B.E., and Schreiber, S.L. 2004. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem. Biol. 11: 295-299.
8. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
9. Lage, J.M., Leamon, J.H., Pejovic, T., Hamann, S., Lacey, M., Dillon, D., Segraves, R., Vossbrinck, B., González, A., Pinkel, D., et al. 2003. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res. 13: 294-307.
10. Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D., and Lieb, J.D. 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36: 900-905.
11. Liu, C.L., Schreiber, S.L., and Bernstein, B.E. 2003. Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4: 19. doi: 10.1186/1471-2164-4-19.
12. Liu, C.L., Bernstein, B.E., and Schreiber, S.L. 2008a. Whole genome amplification by T7-based linear amplification of DNA (TLAD): I. CIP treatment of samples and tailing reaction with terminal transferase. CSH Protocols (this issue) doi: 10.1101/pdb.prot5002.
13. Liu, C.L., Bernstein, B.E., and Schreiber, S.L. 2008b. Whole genome amplification by T7-based linear amplification of DNA (TLAD): II. Second-strand synthesis and in vitro transcription. CSH Protocols (this issue) doi: 10.1101/pdb.prot5003.
14. Liu, C.L., Bernstein, B.E., and Schreiber, S.L. 2008c. Whole genome amplification by T7-based linear amplification of DNA (TLAD): III. Sample purification. CSH Protocols (this issue) doi: 10.1101/ pdb.prot5004.
15. Marko, N.F., Frank, B., Quackenbush, J., and Lee, N.H. 2005. A robust method for the amplification of RNA in the sense orientation. BMC Genomics 6: 27. doi: 10.1186/1471-2164-6-27.
16. Martin, C.T., Muller, D.K., and Coleman, J.E. 1988. Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 27: 3966-3974.
17. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
18. Sambrook, J. and Russell, D.W. 2001. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.