NanoCAGE: A high-resolution technique to discover and interrogate cell transcriptomes

Cold Spring Harbor Protocols

Volumn 6, Issue 1, 2011, Pages

  Salimullah, Md ^a   Mizuho, Sakai ^a   Plessy, Charles ^a   Carninci, Piero ^a  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; RNA DIRECTED DNA POLYMERASE; TRANSCRIPTOME;

ARTICLE; ARTIFACT REDUCTION; CAP ANALYSIS GENE EXPRESSION; CLINICAL PROTOCOL; DNA FLANKING REGION; DNA PURIFICATION; ENZYME INACTIVATION; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; INTERMETHOD COMPARISON; NANOANALYSIS; NANOTECHNOLOGY; PROCESS OPTIMIZATION; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; SENSITIVITY ANALYSIS;

EID: 78651437467     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.prot5559     Document Type: Article

References (11)

1. Carninci P. 2010. Tagging transcription start sites with CAGE. In Cap-analysis gene expression (CAGE): The science of decoding gene transcription (ed. P Carninci), pp. 7-20. Pan Stanford, Singapore.
2. Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M et al. 1996. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37: 327-336.
3. Carninci P, Westover A, Nishiyama Y, Ohsumi T, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Schneider C et al. 1997. High efficiency selection of full-length cDNA by improved biotinylated cap trapper. DNA Res 4: 61-66
4. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CAM, Taylor MS, Engström PG, Frith MC et al. 2006. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
5. Chenchik A, Zhu YY, Diatchenko L, Li R, Hill J, Siebert PD. 1998. Generation and use of high quality cDNA from small amounts of total RNA by SMART™ PCR. In Gene cloning and analysis by RT-PCR (ed. P Siebert, J Larrick), pp. 305-319. Eaton, Natick, MA.
6. Hirzmann J, Luo D, Hahnen J, Hobom G. 1993. Determination of messenger RNA 5'-ends by reverse transcription of the cap structure. Nucleic Acids Res 21: 3597-3598.
7. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M et al. 2006. CAGE: Cap analysis of gene expression. Nat Methods 3: 211-222.
8. Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D et al. 2010. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods 7: 528-534.
9. Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ et al. 2009. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562.
10. Valen E, Sandelin A, Winther O, Krogh A. 2009. Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol 5: e1000562. doi:10.1371/journal.pcbi.1000562
11. Vitezic M, Lassmann T, Forrest ARR, Suzuki M, Tomaru Y, Kawai J, Carninci P, Suzuki H, Hayashizaki Y, Daub CO. 2010. Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. Nucleic Acids Resdoi: 10.1093/nar/gkq729.