利用RNA测序对盘基网柄菌进行转录谱分析。
Transcriptional profiling of Dictyostelium with RNA sequencing.
作者信息
Miranda Edward Roshan, Rot Gregor, Toplak Marko, Santhanam Balaji, Curk Tomaz, Shaulsky Gad, Zupan Blaz
机构信息
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
出版信息
Methods Mol Biol. 2013;983:139-71. doi: 10.1007/978-1-62703-302-2_8.
Abstract
Transcriptional profiling methods have been utilized in the analysis of various biological processes in Dictyostelium. Recent advances in high-throughput sequencing have increased the resolution and the dynamic range of transcriptional profiling. Here we describe the utility of RNA sequencing with the Illumina technology for production of transcriptional profiles. We also describe methods for data mapping and storage as well as common and specialized tools for data analysis, both online and offline.
摘要
转录谱分析方法已被用于分析盘基网柄菌中的各种生物学过程。高通量测序技术的最新进展提高了转录谱分析的分辨率和动态范围。在此，我们描述了利用Illumina技术进行RNA测序以生成转录谱的实用性。我们还描述了数据映射和存储的方法，以及用于在线和离线数据分析的通用和专用工具。
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本文引用的文献
1
Illumina sequencing library preparation for highly multiplexed target capture and sequencing.用于高度多重目标捕获和测序的Illumina测序文库制备。
Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448. doi: 10.1101/pdb.prot5448.
2
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.高多重条码测序：一种用于并行分析混合样本的高效方法。
Nucleic Acids Res. 2010 Jul;38(13):e142. doi: 10.1093/nar/gkq368. Epub 2010 May 11.
3
Conserved developmental transcriptomes in evolutionarily divergent species.进化上差异较大的物种中保守的发育转录组。
Genome Biol. 2010;11(3):R35. doi: 10.1186/gb-2010-11-3-r35. Epub 2010 Mar 17.
4
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.dictyExpress：一个具有探索性数据分析的基于网络界面的盘基网柄菌基因表达数据库。
BMC Bioinformatics. 2009 Aug 25;10:265. doi: 10.1186/1471-2105-10-265.
5
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.短DNA序列与人类基因组的超快速且内存高效比对。
Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.
6
RNA-Seq: a revolutionary tool for transcriptomics.RNA测序：转录组学的革命性工具。
Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484.
7
Stem cell transcriptome profiling via massive-scale mRNA sequencing.通过大规模mRNA测序进行干细胞转录组分析。
Nat Methods. 2008 Jul;5(7):613-9. doi: 10.1038/nmeth.1223. Epub 2008 May 30.
8
The transcriptional landscape of the yeast genome defined by RNA sequencing.通过RNA测序定义的酵母基因组转录图谱。
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9
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Bioinformatics. 2005 Dec 15;21(24):4371-7. doi: 10.1093/bioinformatics/bti726. Epub 2005 Oct 18.
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