Electronic Resource
Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction
| العنوان: | Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction |
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| المؤلفون: | Massachusetts Institute of Technology. Department of Biology, Butty, Vincent L G, Levine, Stuart S., Herbert, Zachary T, Kershner, Jamie P, Thimmapuram, Jyothi, Choudhari, Sulbha, Alekseyev, Yuriy O, Fan, Jun, Podnar, Jessica W, Wilcox, Edward, Gipson, Jenny, Gillaspy, Allison, Jepsen, Kristen, BonDurant, Sandra S, Morris, Krystalynne, Berkeley, Maura, LeClerc, Ashley, Simpson, Stephen D, Sommerville, Gary, Grimmett, Leslie, Adams, Marie |
| المصدر: | BioMed Central |
| بيانات النشر: | BioMed Central Ltd 2018-04-13T19:22:24Z 2018-04-13T19:22:24Z 2018-03 2017-09 2018-03-18T04:12:03Z |
| نوع الوثيقة: | Electronic Resource |
| مستخلص: | Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Keywords: RNAseqr; RNA depletion; Illumina; NGS; ABRF; Transcriptomics National Cancer Institute (U.S.) (Grant P30-CA14051) National Institute of Environmental Health Sciences (Grant P30-ES002109) |
| مصطلحات الفهرس: | Article, http://purl.org/eprint/type/JournalArticle |
| URL: | BMC Genomics |
| الاتاحة: | Open access content. Open access content Creative Commons Attribution http://creativecommons.org/licenses/by/4.0 The Author(s). |
| ملاحظة: | application/pdf English |
| Other Numbers: | MYG oai:dspace.mit.edu:1721.1/114726 1471-2164 Herbert, Zachary T. et al. "Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction" BMC Genomics 19, S2 (March 2018): 199 © 2018 The Author(s) 1141884810 |
| المصدر المساهم: | MASSACHUSETTS INST OF TECHNOL LIBRS From OAIster®, provided by the OCLC Cooperative. |
| رقم الانضمام: | edsoai.on1141884810 |
| قاعدة البيانات: | OAIster |
| الوصف غير متاح. |