Single-tube library preparation for degraded DNA
1.In recent years, massive parallel sequencing has revolutionized the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of...
Published in: | Methods in Ecology and Evolution |
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2018
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Online Access: | https://orbit.dtu.dk/en/publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 https://doi.org/10.1111/2041-210X.12871 https://backend.orbit.dtu.dk/ws/files/134813509/Car_e_et_al_2017_Methods_in_Ecology_and_Evolution.pdf |
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ftdtupubl:oai:pure.atira.dk:publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 2024-09-15T18:01:18+00:00 Single-tube library preparation for degraded DNA Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel-Holger S. Samaniego, Jose A. Wales, Nathan Sicheritz-Pontén, Thomas Gilbert, M. Thomas P. 2018 application/pdf https://orbit.dtu.dk/en/publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 https://doi.org/10.1111/2041-210X.12871 https://backend.orbit.dtu.dk/ws/files/134813509/Car_e_et_al_2017_Methods_in_Ecology_and_Evolution.pdf eng eng https://orbit.dtu.dk/en/publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 info:eu-repo/semantics/openAccess Carøe , C , Gopalakrishnan , S , Vinner , L , Mak , S S T , Sinding , M-H S , Samaniego , J A , Wales , N , Sicheritz-Pontén , T & Gilbert , M T P 2018 , ' Single-tube library preparation for degraded DNA ' , Methods in Ecology and Evolution , vol. 9 , no. 2 . https://doi.org/10.1111/2041-210X.12871 Degraded DNA Illumina sequencing Library preparation Museomics Paleogenomics article 2018 ftdtupubl https://doi.org/10.1111/2041-210X.12871 2024-08-13T00:03:05Z 1.In recent years, massive parallel sequencing has revolutionized the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA. 2.In this study, we compare four Illumina library preparation protocols, including two “single-tube” methods developed for this study with the explicit aim of improving data quality and reducing preparation time and expenses. The methods are tested on grey wolf (Canis lupus) museum specimens. 3.We found single-tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%. 4.Given the advantages of single-tube library preparations, we anticipate these methods will be of considerable interest to the growing field of paleogenomics and other applications investigating degraded DNA. Article in Journal/Newspaper Canis lupus Technical University of Denmark: DTU Orbit Methods in Ecology and Evolution 9 2 410 419 |
institution |
Open Polar |
collection |
Technical University of Denmark: DTU Orbit |
op_collection_id |
ftdtupubl |
language |
English |
topic |
Degraded DNA Illumina sequencing Library preparation Museomics Paleogenomics |
spellingShingle |
Degraded DNA Illumina sequencing Library preparation Museomics Paleogenomics Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel-Holger S. Samaniego, Jose A. Wales, Nathan Sicheritz-Pontén, Thomas Gilbert, M. Thomas P. Single-tube library preparation for degraded DNA |
topic_facet |
Degraded DNA Illumina sequencing Library preparation Museomics Paleogenomics |
description |
1.In recent years, massive parallel sequencing has revolutionized the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA. 2.In this study, we compare four Illumina library preparation protocols, including two “single-tube” methods developed for this study with the explicit aim of improving data quality and reducing preparation time and expenses. The methods are tested on grey wolf (Canis lupus) museum specimens. 3.We found single-tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%. 4.Given the advantages of single-tube library preparations, we anticipate these methods will be of considerable interest to the growing field of paleogenomics and other applications investigating degraded DNA. |
format |
Article in Journal/Newspaper |
author |
Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel-Holger S. Samaniego, Jose A. Wales, Nathan Sicheritz-Pontén, Thomas Gilbert, M. Thomas P. |
author_facet |
Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel-Holger S. Samaniego, Jose A. Wales, Nathan Sicheritz-Pontén, Thomas Gilbert, M. Thomas P. |
author_sort |
Carøe, Christian |
title |
Single-tube library preparation for degraded DNA |
title_short |
Single-tube library preparation for degraded DNA |
title_full |
Single-tube library preparation for degraded DNA |
title_fullStr |
Single-tube library preparation for degraded DNA |
title_full_unstemmed |
Single-tube library preparation for degraded DNA |
title_sort |
single-tube library preparation for degraded dna |
publishDate |
2018 |
url |
https://orbit.dtu.dk/en/publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 https://doi.org/10.1111/2041-210X.12871 https://backend.orbit.dtu.dk/ws/files/134813509/Car_e_et_al_2017_Methods_in_Ecology_and_Evolution.pdf |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Carøe , C , Gopalakrishnan , S , Vinner , L , Mak , S S T , Sinding , M-H S , Samaniego , J A , Wales , N , Sicheritz-Pontén , T & Gilbert , M T P 2018 , ' Single-tube library preparation for degraded DNA ' , Methods in Ecology and Evolution , vol. 9 , no. 2 . https://doi.org/10.1111/2041-210X.12871 |
op_relation |
https://orbit.dtu.dk/en/publications/fa7d161e-7219-41e2-b8c8-eb9aafc20853 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1111/2041-210X.12871 |
container_title |
Methods in Ecology and Evolution |
container_volume |
9 |
container_issue |
2 |
container_start_page |
410 |
op_container_end_page |
419 |
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1810438459578384384 |