A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
<p>Abstract</p> <p>Background</p> <p>Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3’ end adapter containing a 5’,5’-adenyl pyrophosphoryl moiety. In the absence of ATP, this...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2012-09-01
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| Series: | Plant Methods |
| Subjects: | |
| Online Access: | http://www.plantmethods.com/content/8/1/41 |
| _version_ | 1819085464666112000 |
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| author | Chen Yun-Ru Zheng Yi Liu Bao Zhong Silin Giovannoni Jim Fei Zhangjun |
| author_facet | Chen Yun-Ru Zheng Yi Liu Bao Zhong Silin Giovannoni Jim Fei Zhangjun |
| author_sort | Chen Yun-Ru |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3’ end adapter containing a 5’,5’-adenyl pyrophosphoryl moiety. In the absence of ATP, this adapter can be ligated to the 3’ hydroxyl group of small RNA, while RNA self-ligation and concatenation are repressed. Pre-adenylated adapters are one of the most essential and costly components required for library preparation, and few are commercially available.</p> <p>Results</p> <p>We demonstrate that DNA oligo with 5’ phosphate and 3’ amine groups can be enzymatically adenylated by T4 RNA ligase 1 to generate customized pre-adenylated adapters. We have constructed and sequenced a small RNA library for tomato (<it>Solanum lycopersicum</it>) using the T4 RNA ligase 1 adenylated adapter.</p> <p>Conclusion</p> <p>We provide an efficient and low-cost method for small RNA sequencing library preparation, which takes two days to complete and costs around $20 per library. This protocol has been tested in several plant species for small RNA sequencing including sweet potato, pepper, watermelon, and cowpea, and could be readily applied to any RNA samples.</p> |
| first_indexed | 2024-12-21T21:04:46Z |
| format | Article |
| id | doaj.art-0f11f4972d574b26a693872add4640d1 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-21T21:04:46Z |
| publishDate | 2012-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-0f11f4972d574b26a693872add4640d12022-12-21T18:50:19ZengBMCPlant Methods1746-48112012-09-01814110.1186/1746-4811-8-41A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adaptersChen Yun-RuZheng YiLiu BaoZhong SilinGiovannoni JimFei Zhangjun<p>Abstract</p> <p>Background</p> <p>Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3’ end adapter containing a 5’,5’-adenyl pyrophosphoryl moiety. In the absence of ATP, this adapter can be ligated to the 3’ hydroxyl group of small RNA, while RNA self-ligation and concatenation are repressed. Pre-adenylated adapters are one of the most essential and costly components required for library preparation, and few are commercially available.</p> <p>Results</p> <p>We demonstrate that DNA oligo with 5’ phosphate and 3’ amine groups can be enzymatically adenylated by T4 RNA ligase 1 to generate customized pre-adenylated adapters. We have constructed and sequenced a small RNA library for tomato (<it>Solanum lycopersicum</it>) using the T4 RNA ligase 1 adenylated adapter.</p> <p>Conclusion</p> <p>We provide an efficient and low-cost method for small RNA sequencing library preparation, which takes two days to complete and costs around $20 per library. This protocol has been tested in several plant species for small RNA sequencing including sweet potato, pepper, watermelon, and cowpea, and could be readily applied to any RNA samples.</p>http://www.plantmethods.com/content/8/1/41Small RNA sequencingDirectional mRNA sequencing3’ RNA adapterAdenylationT4 RNA ligase 1 |
| spellingShingle | Chen Yun-Ru Zheng Yi Liu Bao Zhong Silin Giovannoni Jim Fei Zhangjun A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters Plant Methods Small RNA sequencing Directional mRNA sequencing 3’ RNA adapter Adenylation T4 RNA ligase 1 |
| title | A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters |
| title_full | A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters |
| title_fullStr | A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters |
| title_full_unstemmed | A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters |
| title_short | A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters |
| title_sort | cost effective method for illumina small rna seq library preparation using t4 rna ligase 1 adenylated adapters |
| topic | Small RNA sequencing Directional mRNA sequencing 3’ RNA adapter Adenylation T4 RNA ligase 1 |
| url | http://www.plantmethods.com/content/8/1/41 |
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