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231226s2023 xx |||||o 00| ||eng c |
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|a 10.1093/jxb/erac515
|2 doi
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|a pubmed24n1169.xml
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|a (DE-627)NLM350971323
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|a (NLM)36585802
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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| 100 |
1 |
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|a Tao, Xiaoyuan
|e verfasserin
|4 aut
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| 245 |
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|a A novel strand-specific RNA-sequencing protocol using dU-adaptor-assembled Tn5
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|c 2023
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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|a Date Completed 30.03.2023
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|a Date Revised 04.04.2023
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|a published: Print
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|a Citation Status MEDLINE
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|a © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissionsoup.com.
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|a Strand-specific RNA-seq is a powerful tool for the discovery of novel transcripts, annotation of genomes, and profiling of gene expression levels. Tn5 transposase has been successfully applied in massive-scale sequencing projects; in particular, Tn5 adaptor modification is used in epigenetics, genomic structure, and chromatin visualization. We developed a novel dU-adaptor-assembled Tn5-mediated strand-specific RNA-sequencing protocol and compared this method with the leading dUTP method in terms of experimental procedure and multiple quality metrics of the generated libraries. The results showed that the dU-Tn5 method is easy to operate and generates a strand-specific RNA-seq library of comparable quality considering library complexity, strand-specificity, evenness, and continuity of annotated transcript coverage. We also evaluated the performance of the dU-Tn5 method in identifying nitrogen-responsive protein-coding genes and long non-coding RNAs in soybean roots. The results indicated that ~62-70% of differentially expressed genes detected from conventional libraries were also detected in dU-Tn5 libraries, indicating good agreement of our method with the current standard; moreover, their fold-changes were highly correlated (R>0.9). Thus, our method provides a promising 'do-it-yourself' stranded RNA-seq procedure for gene expression profiling
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a Tn5
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|a dU-Tn5
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|a dUTP
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|a lncRNA
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| 650 |
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|a soybean
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| 650 |
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|a stranded RNA-seq
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| 650 |
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|a DNA, Complementary
|2 NLM
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| 650 |
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|a Chromatin
|2 NLM
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| 650 |
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|a RNA
|2 NLM
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| 650 |
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|a 63231-63-0
|2 NLM
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| 700 |
1 |
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|a Feng, Shouli
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Li, Sujuan
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Chen, Guang
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Wang, Jian
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Xu, Lizhi
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Fu, Xujun
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Yu, Jing
|e verfasserin
|4 aut
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| 700 |
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|a Xu, Shengchun
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of experimental botany
|d 1985
|g 74(2023), 6 vom: 28. März, Seite 1806-1820
|w (DE-627)NLM098182706
|x 1460-2431
|7 nnns
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| 773 |
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|g volume:74
|g year:2023
|g number:6
|g day:28
|g month:03
|g pages:1806-1820
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| 856 |
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|u http://dx.doi.org/10.1093/jxb/erac515
|3 Volltext
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