TELP, a sensitive and versatile library construction method for next-generation sequencing

Nucleic Acids Research

Volumn 43, Issue 6, 2015, Pages e35-

  Peng, Xu ^a   Wu, Jingyi ^b   Brunmeir, Reinhard ^a   Kim, Sun Yee ^a   Zhang, Qiongyi ^a   Ding, Chunming ^a   Han, Weiping ^c,d   Xie, Wei ^b   Xu, Feng ^a,d  

^a AGENCY FOR SCIENCE   (Singapore)

^b PEKING UNIVERSITY   (China)

^c AGENCY FOR SCIENCE   (Singapore)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA; DNA; RNA; TRANSCRIPTOME;

ADIPOCYTE; ADIPOGENESIS; ANIMAL CELL; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA LIBRARY; DNA PURIFICATION; EPIGENETICS; GENE EXPRESSION; HISTONE MODIFICATION; INSTRUMENT VALIDATION; MOUSE; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; ANIMAL; CYTOLOGY; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS;

ADIPOCYTES; ADIPOGENESIS; ANIMALS; CHROMATIN IMMUNOPRECIPITATION; DNA; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; RNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84937212099     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku818     Document Type: Article

References (33)

1. Park,P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
2. Levin,J.Z., Yassour,M., Adiconis,X., Nusbaum,C., Thompson,D.A., Friedman,N., Gnirke,A. and Regev,A. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods, 7, 709-715.
3. Farmer,S.R. (2006) Transcriptional control of adipocyte formation. Cell Metab., 4, 263-273.
4. Tontonoz,P., Hu,E. and Spiegelman,B.M. (1994) Stimulation of adipogenesis in fibroblasts by PPAR gamma 2, a lipid-activated transcription factor. Cell, 79, 1147-1156.
5. Tontonoz,P. and Spiegelman,B.M. (2008) Fat and beyond: the diverse biology of PPARgamma. Annu. Rev. Biochem., 77, 289-312.
6. Zhang,Q., Ramlee,M.K., Brunmeir,R., Villanueva,C.J., Halperin,D. and Xu,F. (2012) Dynamic and distinct histone modifications modulate the expression of key adipogenesis regulatory genes. Cell Cycle, 11, 4310-4322.
7. Mikkelsen,T.S., Xu,Z., Zhang,X., Wang,L., Gimble,J.M., Lander,E.S. and Rosen,E.D. (2011) Comparative epigenomic analysis of murine and human adipogenesis. Cell, 143, 156-169.
8. Shechter,D., Dormann,H.L., Allis,C.D. and Hake,S.B. (2007) Extraction, purification and analysis of histones. Nat. Protoc., 2, 1445-1457.
9. Laborda,J. (1991) 36B4 cDNA used as an estradiol-independent mRNA control is the cDNA for human acidic ribosomal phosphoprotein PO. Nucleic Acids Res., 19, 3998.
10. Zhang,Y., Liu,T., Meyer,C.A., Eeckhoute,J., Johnson,D.S., Bernstein,B.E., Nusbaum,C., Myers,R.M., Brown,M., Li,W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
11. 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.
12. Siersbaek,M.S., Loft,A., Aagaard,M.M., Nielsen,R., Schmidt,S.F., Petrovic,N., Nedergaard,J. and Mandrup,S. (2012) Genome-wide profiling of peroxisome proliferator-activated receptor gamma in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression. Mol. Cell Biol., 32, 3452-3463.
13. Santos-Rosa,H., Schneider,R., Bannister,A.J., Sherriff,J., Bernstein,B.E., Emre,N.C., Schreiber,S.L., Mellor,J. and Kouzarides,T. (2002) Active genes are tri-methylated at K4 of histone H3. Nature, 419, 407-411.
14. Cao,R., Wang,L., Wang,H., Xia,L., Erdjument-Bromage,H., Tempst,P., Jones,R.S. and Zhang,Y. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science, 298, 1039-1043.
15. Xu,F., Zhang,K. and Grunstein,M. (2005) Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell, 121, 375-385.
16. Li,B., Carey,M. and Workman,J.L. (2007) The role of chromatin during transcription. Cell, 128, 707-719.
17. Agalioti,T., Chen,G. and Thanos,D. (2002) Deciphering the transcriptional histone acetylation code for a human gene. Cell, 111, 381-392.
18. Heintzman,N.D., Stuart,R.K., Hon,G., Fu,Y., Ching,C.W., Hawkins,R.D., Barrera,L.O., Van Calcar,S., Qu,C., Ching,K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39, 311-318.
19. Creyghton,M.P., Cheng,A.W., Welstead,G.G., Kooistra,T., Carey,B.W., Steine,E.J., Hanna,J., Lodato,M.A., Frampton,G.M., Sharp,P.A. et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. U.S.A., 107, 21931-21936.
20. Rada-Iglesias,A., Bajpai,R., Swigut,T., Brugmann,S.A., Flynn,R.A. and Wysocka,J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature, 470, 279-283.
21. Core,L.J., Waterfall,J.J. and Lis,J.T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
22. Parkhomchuk,D., Borodina,T., Amstislavskiy,V., Banaru,M., Hallen,L., Krobitsch,S., Lehrach,H. and Soldatov,A. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res., 37, e123.
23. He,Y., Vogelstein,B., Velculescu,V.E., Papadopoulos,N. and Kinzler,K.W. (2008) The antisense transcriptomes of human cells. Science, 322, 1855-1857.
24. Gansauge,M.T. and Meyer,M. (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc., 8, 737-748.
25. Meyer,M., Kircher,M., Gansauge,M.T., Li,H., Racimo,F., Mallick,S., Schraiber,J.G., Jay,F., Prufer,K., de Filippo,C. et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222-226.
26. Shankaranarayanan,P., Mendoza-Parra,M.A., Walia,M., Wang,L., Li,N., Trindade,L.M. and Gronemeyer,H. (2011) Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat. Methods, 8, 565-567.
27. Adli,M., Zhu,J. and Bernstein,B.E. (2010) Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods, 7, 615-618.
28. Ng,J.H., Kumar,V., Muratani,M., Kraus,P., Yeo,J.C., Yaw,L.P., Xue,K., Lufkin,T., Prabhakar,S. and Ng,H.H. (2013) In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Dev. Cell, 24, 324-333.
29. Zhou,Z.X., Zhang,M.J., Peng,X., Takayama,Y., Xu,X.Y., Huang,L.Z. and Du,L.L. (2013) Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method. Genome Res., 23, 705-715.
30. Acevedo,L.G., Iniguez,A.L., Holster,H.L., Zhang,X., Green,R. and Farnham,P.J. (2007) Genome-scale ChIP-chip analysis using 10,000 human cells. BioTechniques, 43, 791-797.
31. Dahl,J.A. and Collas,P. (2008) MicroChIP-a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Res., 36, e15.
32. Wu,A.R., Hiatt,J.B., Lu,R., Attema,J.L., Lobo,N.A., Weissman,I.L., Clarke,M.F. and Quake,S.R. (2009) Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab Chip, 9, 1365-1370.
33. O'Neill,L.P., VerMilyea,M.D. and Turner,B.M. (2006) Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet., 38, 835-841.