Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease

Current Protocols in Molecular Biology

Volumn , Issue SUPPL.94, 2011, Pages

  Christodoulou, Danos C ^a   Gorham, Joshua M ^a   Herman, Daniel S ^a   Seidman, J G ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Crab duplex nuclease; High throughput DNA sequencing; Library normalization; RNA seq

Indexed keywords

AGAROSE; COMPLEMENTARY DNA; CRAB DUPLEX SPECIFIC NUCLEASE; DOUBLE STRANDED DNA; DYE; NUCLEASE; POLYACRYLAMIDE GEL; POLYADENYLATED RNA; SYBR GOLD; UNCLASSIFIED DRUG;

ARTICLE; CONTAMINATION; DEVICE; DNA DENATURATION; DNA EXTRACTION; EXPRESSED SEQUENCE TAG; GENE AMPLIFICATION; HYBRIDIZATION; ILLUMINATION; INCUBATION TEMPERATURE; INCUBATION TIME; MOLECULAR LIBRARY; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PURIFICATION; REAL TIME POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA FRAGMENTATION; RNA SEQ LIBRARY; RNA SEQUENCE; SEQUENCE ANALYSIS; ULTRAVIOLET IRRADIATION; UV TRANSILLUMINATOR;

DECAPODA (CRUSTACEA);

EID: 84857656651     PISSN: 19343639     EISSN: 19343647     Source Type: Journal    
DOI: 10.1002/0471142727.mb0412s94     Document Type: Article

References (10)

1. Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown,M.K., Taylor, D.F., Steptoe, A.L., Wani, S., Bethel, G., Robertson, A.J., Perkins, A.C., Bruce, S.J., Lee, C.C., Ranade, S.S., Peckham, H.E., Manning, J.M., McKernan, K.J., and Grimmond, S.M. 2008. Stem cell transcriptome profiling via massivescale mRNA sequencing. Nat. Methods 5:613-619.
2. 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.
3. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:621-628.
4. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., and Snyder, M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349.
5. Schroeder, A., Mueller, O., Stocker, S., Salowsky, R., Leiber, M., Gassmann, M., Lightfoot, S., Menzel, W., Granzow, M., and Ragg, T. 2006. The RIN: An RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 7:3.
6. Sultan, M., Schulz, M.H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O'Keeffe, S., Haas, S., Vingron, M., Lehrach,H., andYaspo, M.L. 2008.Aglobal view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956-960.
7. Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A., Lao, K., and Surani, M.A. 2009. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6:377-382.
8. Trapnell, C.,Williams, B.A., Pertea, G.,Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511-515.
9. Wang, E.T. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476.
10. Zhulidov, P.A., Bogdanova, E.A., Shcheglov, A.S., Vagner, L.L., Khaspekov, G.L., Kozhemyako, V.B., Matz, M.V., Meleshkevitch, E., Moroz, L.L., Lukyanov, S.A., and Shagin, D.A. 2004. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res. 32:e37.