Analysis of EBV Transcription Using High-Throughput RNA Sequencing.

[en] High-throughput sequencing of RNA is used to analyze the transcriptomes of viruses and cells, providing information about transcript structure and abundance. A wide array of programs and pipelines has been created to manage and interpret the abundance of data generated from high-throughput RNA sequencing experiments. This protocol details the use of free and open-source programs to align RNA-Seq reads to a reference genome, visualize read coverage and splice junctions, estimate transcript abundance, and evaluate differential expression of transcripts in different conditions. Particular concerns related to EBV and viral transcriptomics are addressed and access to EBV reference files is provided.

Disciplines :

Human health sciences: Multidisciplinary, general & others

Author, co-author :

O'Grady, Tina ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et biologie moléculaires animales

Baddoo, Melody

Flemington, Erik K.

Language :

English

Title :

Analysis of EBV Transcription Using High-Throughput RNA Sequencing.

Publication date :

2017

Journal title :

Methods in Molecular Biology

ISSN :

1064-3745

eISSN :

1940-6029

Publisher :

Humana Press, Clifton, United States - New Jersey

Volume :

1532

Pages :

105-121

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 17 January 2018

Statistics

Number of views

276 (2 by ULiège)

Number of downloads

859 (6 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

Bibliography

Kurosawa, J., Nishiyori, H., Hayashizaki, Y., Deep cap analysis of gene expression (2011) Methods Mol Biol, 687, pp. 147-163
Zhao, J., Ohsumi, T.K., Kung, J.T., Ogawa, Y., Grau, D.J., Sarma, K., Song, J.J., Lee, J.T., Genome-wide identification of polycomb-associated RNAs by RIP-seq (2010) Mol Cell, 40 (6), pp. 939-953. , S1097-2765(10)00967-6 [pii]
Core, L.J., Waterfall, J.J., Lis, J.T., Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters (2008) Science, 322 (5909), pp. 1845-1848. , 1162228 [pii]
Ingolia, N.T., Genome-wide translational profiling by ribosome footprinting (2010) Methods Enzymol, 470, pp. 119-142. , S0076- 6879(10)70006-9[pii]
Gatherer, D., Seirafian, S., Cunningham, C., Holton, M., Dargan, D.J., Baluchova, K., Hector, R.D., Davison, A.J., High-resolution human cytomegalovirus transcriptome (2011) Proc Natl Acad Sci U S A, 108 (49), pp. 19755-19760. , 1115861108[pii]
Concha, M., Wang, X., Cao, S., Baddoo, M., Fewell, C., Lin, Z., Hulme, W., Flemington, E.K., Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNASeq (2012) J Virol, 86 (3), pp. 1458-1467. , JVI.06537-11 [pii]
Arias, C., Weisburd, B., Stern-Ginossar, N., Mercier, A., Madrid, A.S., Bellare, P., Holdorf, M., Ganem, D., KSHV 2.0: A comprehensive annotation of the Kaposi’s sarcoma- associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features (2014) PLoS Pathog, 10 (1)
O’Grady, T., Cao, S., Strong, M.J., Concha, M., Wang, X., Splinter Bondurant, S., Adams, M., Flemington, E.K., Global bidirectional transcription of the Epstein-Barr virus genome during reactivation (2014) J Virol, 88 (3), pp. 1604-1616. , JVI.02989-13 [pii]
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Gingeras, T.R., STAR: Ultrafast universal RNA-seq aligner (2013) Bioinformatics, 29 (1), pp. 15-21. , bts635 [pii]
Thorvaldsdottir, H., Robinson, J.T., Mesirov, J.P., Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration (2013) Brief Bioinform, 14 (2), pp. 178-192. , bbs017 [pii]
Li, B., Dewey, C.N., RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome (2011) BMC Bioinformatics, 12, p. 323. , 1471-2105-12-323 [pii]
Leng, N., Dawson, J.A., Thomson, J.A., Ruotti, V., Rissman, A.I., Smits, B.M., Haag, J.D., Kendziorski, C., EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments (2013) Bioinformatics, 29 (8), pp. 1035-1043. , btt087 [pii]
Lin, Z., Wang, X., Strong, M.J., Concha, M., Baddoo, M., Xu, G., Baribault, C., Flemington, E.K., Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains (2013) J Virol, 87 (2), pp. 1172-1182. , JVI.02517-12 [pii]