Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

被引：392

作者：

Gansauge, Marie-Theres ^{[1
]}

Meyer, Matthias ^{[1
]}

机构：

[1] Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany

来源：

NATURE PROTOCOLS | 2013年 / 8卷 / 04期

关键词：

GENOME SEQUENCE; SHORT-READ; RETRIEVAL; LIGATION;

D O I：

10.1038/nprot.2013.038

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of short or degraded DNA from other sources, and it can also be used for sequencing oligonucleotides. Single-stranded library preparation is performed by ligating a biotinylated adapter oligonucleotide to the 3' ends of heat-denatured DNA. The resulting strands are then immobilized on streptavidin-coated beads and copied with a polymerase. A second adapter is attached by blunt-end ligation, and library preparation is completed by PCR amplification. We estimate that intact DNA strands are recovered in the library with similar to 50% efficiency. Libraries can be generated from up to 12 DNA or oligonucleotide samples in parallel within 2 d.

引用

页码：737 / 748

页数：12

共 32 条

[1]

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition [J].

Adey, Andrew ;

Morrison, Hilary G. ;

Asan ;

Xun, Xu ;

Kitzman, Jacob O. ;

Turner, Emily H. ;

Stackhouse, Bethany ;

MacKenzie, Alexandra P. ;

Caruccio, Nicholas C. ;

Zhang, Xiuqing ;

Shendure, Jay .

GENOME BIOLOGY, 2010, 11 (12)

[2]

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA [J].

Avila-Arcos, Maria C. ;

Cappellini, Enrico ;

Alberto Romero-Navarro, J. ;

Wales, Nathan ;

Victor Moreno-Mayar, J. ;

Rasmussen, Morten ;

Fordyce, Sarah L. ;

Montiel, Rafael ;

Vielle-Calzada, Jean-Philippe ;

Willerslev, Eske ;

Gilbert, M. Thomas P. .

SCIENTIFIC REPORTS, 2011, 1

[3]

Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[4]

Patterns of damage in genomic DNA sequences from a Neandertal [J].

Briggs, Adrian W. ;

Stenzel, Udo ;

Johnson, Philip L. F. ;

Green, Richard E. ;

Kelso, Janet ;

Pruefer, Kay ;

Meyer, Matthias ;

Krause, Johannes ;

Ronan, Michael T. ;

Lachmann, Michael ;

Paeaebo, Svante .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (37) :14616-14621

[5]

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA [J].

Briggs, Adrian W. ;

Stenzel, Udo ;

Meyer, Matthias ;

Krause, Johannes ;

Kircher, Martin ;

Paeaebo, Svante .

NUCLEIC ACIDS RESEARCH, 2010, 38 (06) :e87.1-e87.12

[6]

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes [J].

Briggs, Adrian W. ;

Good, Jeffrey M. ;

Green, Richard E. ;

Krause, Johannes ;

Maricic, Tomislav ;

Stenzel, Udo ;

Lalueza-Fox, Carles ;

Rudan, Pavao ;

Brajkovic, Dejana ;

Kucan, Zeljko ;

Gusic, Ivan ;

Schmitz, Ralf ;

Doronichev, Vladimir B. ;

Golovanova, Liubov V. ;

de la Rasilla, Marco ;

Fortea, Javier ;

Rosas, Antonio ;

Paeaebo, Svante .

SCIENCE, 2009, 325 (5938) :318-321

[7]

Novel high-resolution characterization of ancient DNA reveals C>U-type base modification events as the sole cause of post mortem miscoding lesions [J].

Brotherton, Paul ;

Endicott, Phillip ;

Sanchez, Juan J. ;

Beaumont, Mark ;

Barnett, Ross ;

Austin, Jeremy ;

Cooper, Alan .

NUCLEIC ACIDS RESEARCH, 2007, 35 (17) :5717-5728

[8]

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture [J].

Burbano, Hernan A. ;

Hodges, Emily ;

Green, Richard E. ;

Briggs, Adrian W. ;

Krause, Johannes ;

Meyer, Matthias ;

Good, Jeffrey M. ;

Maricic, Tomislav ;

Johnson, Philip L. F. ;

Xuan, Zhenyu ;

Rooks, Michelle ;

Bhattacharjee, Arindam ;

Brizuela, Leonardo ;

Albert, Frank W. ;

de la Rasilla, Marco ;

Fortea, Javier ;

Rosas, Antonio ;

Lachmann, Michael ;

Hannon, Gregory J. ;

Paeaebo, Svante .

SCIENCE, 2010, 328 (5979) :723-725

[9]

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications [J].

Champlot, Sophie ;

Berthelot, Camille ;

Pruvost, Melanie ;

Bennett, E. Andrew ;

Grange, Thierry ;

Geigl, Eva-Maria .

PLOS ONE, 2010, 5 (09)

[10]

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries [J].

Dabney, Jesse ;

Meyer, Matthias .

BIOTECHNIQUES, 2012, 52 (02) :87-+

← 1 2 3 4 →