Decreasing miRNA sequencing bias using a single adapter and circularization approach

被引：39

作者：

Barberan-Soler, Sergio ^{[1
]}

Vo, Jenny M. ^{[1
]}

Hogans, Ryan E. ^{[1
]}

Dallas, Anne ^{[1
]}

Johnston, Brian H. ^{[1
]}

Kazakov, Sergei A. ^{[1
]}

机构：

[1] SomaGenics Inc, Santa Cruz, CA 95060 USA

来源：

GENOME BIOLOGY | 2018年 / 19卷

关键词：

miRNA-seq; Sequencing bias; Small RNA sequencing; Small RNA library preparation; RNA LIBRARY PREPARATION; MICRORNAS; LIGASE;

D O I：

10.1186/s13059-018-1488-z

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq (R)-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq (R)-AC provides greatly reduced miRNA sequencing bias and allows the identification of the largest variety of miRNAs in biological samples. This reduced bias also allows robust quantification of miRNAs present in samples across a wide range of RNA input levels.

引用

页数：9

共 35 条

[11] The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Ingolia, Nicholas T.
Brar, Gloria A.
Rouskin, Silvia
McGeachy, Anna M.
Weissman, Jonathan S.
[J]. NATURE PROTOCOLS, 2012, 7 (08) : 1534 - 1550
[12] Evaluating bias-reducing protocols for RNA sequencing library preparation
Jackson, Thomas J.
Spriggs, Ruth V.
Burgoyne, Nicholas J.
Jones, Carolyn
Willis, Anne E.
[J]. BMC GENOMICS, 2014, 15
[13] Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing
Jayaprakash, Anitha D.
Jabado, Omar
Brown, Brian D.
Sachidanandam, Ravi
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 (21) : e141
[14] iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Konig, Julian
Zarnack, Kathi
Rot, Gregor
Curk, Tomaz
Kayikci, Melis
Zupan, Blaz
Turner, Daniel J.
Luscombe, Nicholas M.
Ule, Jernej
[J]. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, 2011, (50):
[15] miRBase: annotating high confidence microRNAs using deep sequencing data
Kozomara, Ana
Griffiths-Jones, Sam
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D68 - D73
[16] miR-ID: A novel, circularization-based platform for detection of microRNAs
Kumar, Pavan
Johnston, Brian H.
Kazakov, Sergei A.
[J]. RNA, 2011, 17 (02) : 365 - 380
[17] Small RNA library preparation for next-generation sequencing by single ligation, extension and circularization technology
Kwon, Young-Soo
[J]. BIOTECHNOLOGY LETTERS, 2011, 33 (08) : 1633 - 1641
[18] Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
Lamm, Ayelet T.
Stadler, Michael R.
Zhang, Huibin
Gent, Jonathan I.
Fire, Andrew Z.
[J]. GENOME RESEARCH, 2011, 21 (02) : 265 - 275
[19] Langmead B, 2012, NAT METHODS, V9, P357, DOI [10.1038/NMETH.1923, 10.1038/nmeth.1923]
[20] Differences in microRNA detection levels are technology and sequence dependent
Leshkowitz, Dena
Horn-Saban, Shirley
Parmet, Yisrael
Feldmesser, Ester
[J]. RNA, 2013, 19 (04) : 527 - 538

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