Matches in SemOpenAlex for { <https://semopenalex.org/work/W4311455428> ?p ?o ?g. }
Showing items 1 to 88 of
88
with 100 items per page.
- W4311455428 abstract "Summary Unless some dedicated treatments are applied, virome shotgun sequencing will only reveal the double stranded DNA (dsDNA) content of a given sample. However bacterial virus genomes often consist of a circular single stranded DNA (ssDNA) molecule. Pre-treatment and amplification of DNA with the multiple displacement amplification (MDA) method allows to convert the ssDNA to ds DNA, but it introduces an over-representation of these circular ssDNA genomes. A more recent alternative consists in using an xGen kit, which permits the ligation of adaptators directly to sheared DNA. However, this kit is expensive, and the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. This prompted us to search for an alternative method of DNA preparation for the sequencing of mixed ssDNA and dsDNA viromes. We present here this new method based on the use of the T7 DNA polymerase (T7pol), which is easy to implement and cheap, and compare it to MDA with 30 minutes incubation time (sMDA) and to the direct shearing of DNA without prior conversion of ssDNA to dsDNA. All samples were then prepared with the xGen kit. We found that sMDA overamplifies with 2 to 8.6-fold excess compared to input phage particles, which was less than reported for the full time, 90 minutes MDA treatment. In contrast, the T7pol method led to the under-representation (1.3 to 8.2-fold) of these genomes, and was overall a better reflection of input phage cocktails, compared to the other methods. We conclude a T7pol pre-treatment is a good alternative to MDA for the shotgun sequencing of viromes." @default.
- W4311455428 created "2022-12-26" @default.
- W4311455428 creator A5007212973 @default.
- W4311455428 creator A5021536595 @default.
- W4311455428 creator A5026626624 @default.
- W4311455428 creator A5042021305 @default.
- W4311455428 creator A5056166425 @default.
- W4311455428 creator A5080451357 @default.
- W4311455428 date "2022-12-14" @default.
- W4311455428 modified "2023-10-18" @default.
- W4311455428 title "An alternative method to multiple displacement amplification for preparing virome DNA in a way adapted for the sequencing of both double-strand and single-strand DNA viruses" @default.
- W4311455428 cites W1539741116 @default.
- W4311455428 cites W1575228817 @default.
- W4311455428 cites W1976313814 @default.
- W4311455428 cites W2017887852 @default.
- W4311455428 cites W2051509901 @default.
- W4311455428 cites W2103441770 @default.
- W4311455428 cites W2110927099 @default.
- W4311455428 cites W2121304902 @default.
- W4311455428 cites W2212839276 @default.
- W4311455428 cites W2560014131 @default.
- W4311455428 cites W2770282499 @default.
- W4311455428 cites W2796529794 @default.
- W4311455428 cites W2904250115 @default.
- W4311455428 cites W2951912016 @default.
- W4311455428 cites W3033129278 @default.
- W4311455428 cites W3081166727 @default.
- W4311455428 cites W3114961285 @default.
- W4311455428 cites W3123925201 @default.
- W4311455428 cites W3127656915 @default.
- W4311455428 cites W3179027382 @default.
- W4311455428 cites W3205258179 @default.
- W4311455428 cites W3210553309 @default.
- W4311455428 cites W4293040420 @default.
- W4311455428 cites W4303457046 @default.
- W4311455428 doi "https://doi.org/10.1101/2022.12.12.520144" @default.
- W4311455428 hasPublicationYear "2022" @default.
- W4311455428 type Work @default.
- W4311455428 citedByCount "1" @default.
- W4311455428 countsByYear W43114554282023 @default.
- W4311455428 crossrefType "posted-content" @default.
- W4311455428 hasAuthorship W4311455428A5007212973 @default.
- W4311455428 hasAuthorship W4311455428A5021536595 @default.
- W4311455428 hasAuthorship W4311455428A5026626624 @default.
- W4311455428 hasAuthorship W4311455428A5042021305 @default.
- W4311455428 hasAuthorship W4311455428A5056166425 @default.
- W4311455428 hasAuthorship W4311455428A5080451357 @default.
- W4311455428 hasBestOaLocation W43114554281 @default.
- W4311455428 hasConcept C104317684 @default.
- W4311455428 hasConcept C141231307 @default.
- W4311455428 hasConcept C153911025 @default.
- W4311455428 hasConcept C156385826 @default.
- W4311455428 hasConcept C190743605 @default.
- W4311455428 hasConcept C49105822 @default.
- W4311455428 hasConcept C51679486 @default.
- W4311455428 hasConcept C54355233 @default.
- W4311455428 hasConcept C552990157 @default.
- W4311455428 hasConcept C70721500 @default.
- W4311455428 hasConcept C78063203 @default.
- W4311455428 hasConcept C86803240 @default.
- W4311455428 hasConceptScore W4311455428C104317684 @default.
- W4311455428 hasConceptScore W4311455428C141231307 @default.
- W4311455428 hasConceptScore W4311455428C153911025 @default.
- W4311455428 hasConceptScore W4311455428C156385826 @default.
- W4311455428 hasConceptScore W4311455428C190743605 @default.
- W4311455428 hasConceptScore W4311455428C49105822 @default.
- W4311455428 hasConceptScore W4311455428C51679486 @default.
- W4311455428 hasConceptScore W4311455428C54355233 @default.
- W4311455428 hasConceptScore W4311455428C552990157 @default.
- W4311455428 hasConceptScore W4311455428C70721500 @default.
- W4311455428 hasConceptScore W4311455428C78063203 @default.
- W4311455428 hasConceptScore W4311455428C86803240 @default.
- W4311455428 hasLocation W43114554281 @default.
- W4311455428 hasOpenAccess W4311455428 @default.
- W4311455428 hasPrimaryLocation W43114554281 @default.
- W4311455428 hasRelatedWork W1991107912 @default.
- W4311455428 hasRelatedWork W2014982185 @default.
- W4311455428 hasRelatedWork W2037912916 @default.
- W4311455428 hasRelatedWork W2084241355 @default.
- W4311455428 hasRelatedWork W2092551624 @default.
- W4311455428 hasRelatedWork W2101878615 @default.
- W4311455428 hasRelatedWork W2119859604 @default.
- W4311455428 hasRelatedWork W3023436389 @default.
- W4311455428 hasRelatedWork W3182597671 @default.
- W4311455428 hasRelatedWork W4282926623 @default.
- W4311455428 isParatext "false" @default.
- W4311455428 isRetracted "false" @default.
- W4311455428 workType "article" @default.