Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens
<p>Abstract</p> <p>Background</p> <p>The Ahringer <it>C. elegans </it>RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by dire...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-03-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/170 |
| _version_ | 1818021666307964928 |
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| author | Lu Yiming Hang Xingyi Wang Xiaolei Zhang Jiye Shi Jinping Li Yuan Ren Changhong Qu Wubin Zhao Dongsheng Zhang Chenggang |
| author_facet | Lu Yiming Hang Xingyi Wang Xiaolei Zhang Jiye Shi Jinping Li Yuan Ren Changhong Qu Wubin Zhao Dongsheng Zhang Chenggang |
| author_sort | Lu Yiming |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The Ahringer <it>C. elegans </it>RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1) mis-annotation (the clone with the retired gene name should be remapped to the actual target gene); 2) nonspecific PCR amplification; 3) cross-RNAi; 4) mis-operation such as sample loading error, <it>etc</it>.</p> <p>Results</p> <p>Here we performed a reliability analysis on the Ahringer <it>C. elegans </it>RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3%) of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54%) bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs). The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (<url>http://biocompute.bmi.ac.cn/CelRNAi/</url>) was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies.</p> <p>Conclusions</p> <p>Because of the potential unreliability of the Ahringer <it>C. elegans </it>RNAi feeding library, we strongly suggest the user examine the reliability information of the bacterial strains in the CelRNAi database before performing RNAi experiments, as well as the post-RNAi experiment analysis.</p> |
| first_indexed | 2024-04-14T08:20:55Z |
| format | Article |
| id | doaj.art-631a00314a7b41ae8d112be6fece60af |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-14T08:20:55Z |
| publishDate | 2011-03-01 |
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| spelling | doaj.art-631a00314a7b41ae8d112be6fece60af2022-12-22T02:04:12ZengBMCBMC Genomics1471-21642011-03-0112117010.1186/1471-2164-12-170Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screensLu YimingHang XingyiWang XiaoleiZhang JiyeShi JinpingLi YuanRen ChanghongQu WubinZhao DongshengZhang Chenggang<p>Abstract</p> <p>Background</p> <p>The Ahringer <it>C. elegans </it>RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1) mis-annotation (the clone with the retired gene name should be remapped to the actual target gene); 2) nonspecific PCR amplification; 3) cross-RNAi; 4) mis-operation such as sample loading error, <it>etc</it>.</p> <p>Results</p> <p>Here we performed a reliability analysis on the Ahringer <it>C. elegans </it>RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3%) of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54%) bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs). The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (<url>http://biocompute.bmi.ac.cn/CelRNAi/</url>) was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies.</p> <p>Conclusions</p> <p>Because of the potential unreliability of the Ahringer <it>C. elegans </it>RNAi feeding library, we strongly suggest the user examine the reliability information of the bacterial strains in the CelRNAi database before performing RNAi experiments, as well as the post-RNAi experiment analysis.</p>http://www.biomedcentral.com/1471-2164/12/170 |
| spellingShingle | Lu Yiming Hang Xingyi Wang Xiaolei Zhang Jiye Shi Jinping Li Yuan Ren Changhong Qu Wubin Zhao Dongsheng Zhang Chenggang Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens BMC Genomics |
| title | Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens |
| title_full | Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens |
| title_fullStr | Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens |
| title_full_unstemmed | Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens |
| title_short | Reliability analysis of the Ahringer <it>Caenorhabditis elegans </it>RNAi feeding library: a guide for genome-wide screens |
| title_sort | reliability analysis of the ahringer it caenorhabditis elegans it rnai feeding library a guide for genome wide screens |
| url | http://www.biomedcentral.com/1471-2164/12/170 |
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