Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations.
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations.
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DOI：
10.3791/54090
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发表时间：
2016-08-04
期刊：
影响因子：
--
通讯作者：
Roychowdhury S
中科院分区：
文献类型：
--
作者：
Martin DP;Miya J;Reeser JW;Roychowdhury S
RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 – 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
14.9
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Tang X;Baheti S;Shameer K;Thompson KJ;Wills Q;Niu N;Holcomb IN;Boutet SC;Ramakrishnan R;Kachergus JM;Kocher JP;Weinshilboum RM;Wang L;Thompson EA;Kalari KR
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5.8
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Novo, Francisco J.
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12.3
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Fernandez-Cuesta L;Sun R;Menon R;George J;Lorenz S;Meza-Zepeda LA;Peifer M;Plenker D;Heuckmann JM;Leenders F;Zander T;Dahmen I;Koker M;Schöttle J;Ullrich RT;Altmüller J;Becker C;Nürnberg P;Seidel H;Böhm D;Göke F;Ansén S;Russell PA;Wright GM;Wainer Z;Solomon B;Petersen I;Clement JH;Sänger J;Brustugun OT;Helland Å;Solberg S;Lund-Iversen M;Buettner R;Wolf J;Brambilla E;Vingron M;Perner S;Haas SA;Thomas RK
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Thomas RK
影响因子：
12.3
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Kim D;Pertea G;Trapnell C;Pimentel H;Kelley R;Salzberg SL
通讯作者：
Salzberg SL