Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
Abstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2017-04-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-017-01165-w |
| _version_ | 1819039936134774784 |
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| author | Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang |
| author_facet | Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang |
| author_sort | Zhibiao Mai |
| collection | DOAJ |
| description | Abstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads. |
| first_indexed | 2024-12-21T09:01:07Z |
| format | Article |
| id | doaj.art-6658cb2a6d154f31904cc68f248dfdad |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-21T09:01:07Z |
| publishDate | 2017-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-6658cb2a6d154f31904cc68f248dfdad2022-12-21T19:09:27ZengNature PortfolioScientific Reports2045-23222017-04-017111010.1038/s41598-017-01165-wLow-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor SequencingZhibiao Mai0Chuanle Xiao1Jingjie Jin2Gong Zhang3Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan UniversityKey Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan UniversityKey Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan UniversityKey Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan UniversityAbstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads.https://doi.org/10.1038/s41598-017-01165-w |
| spellingShingle | Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing Scientific Reports |
| title | Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing |
| title_full | Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing |
| title_fullStr | Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing |
| title_full_unstemmed | Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing |
| title_short | Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing |
| title_sort | low cost low bias and low input rna seq with high experimental verifiability based on semiconductor sequencing |
| url | https://doi.org/10.1038/s41598-017-01165-w |
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