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Accessory files for RNA-seq based EBV transcriptome analysis:

O'Grady, T, Wang, X, Honer Zu Bentrup, K, Baddoo, M, Concha, M, Flemington, EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res. 2016 Jul 12. Pii:gkw629. PMCID:

O’Grady, T, Cao, S, Strong, MJ, Concha, M, Wang, X, Splinter BonDurant, S, Adams, M, Baddoo, M, Srivastav, SK, Lin, Z, Fewell, C, Yin, Q, and Flemington, EK. Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol. 2014 88: 1604-1616. PMCID: PMC3911580

Lin, Z, Wang, X, Strong, MJ, Concha, M, Baddoo, M, Xu, G, Baribault, C, Fewell, C, Hulme, W, Hedges, D, Taylor, CM, Flemington, EK. Whole genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol. 2012: 87:1172-82. (PMID: 23152513).

Concha, M, Wang, X, Cao, S, Baddoo, M, Fewell, C, Lin, Z, Hulme, W, Hedges, D, McBride, J, Flemington, EK. Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-seq. J Virol. 2011 Nov 16. (PMID:22090128). [Epub ahead of print]

Lin, Z, Xu, G, Deng, N, Taylor, C, Zhu, D, Flemington, EK. Quantitative and qualitative RNA-seq based evaluation of Epstein-Barr virus transcription in type I latency Burkitt’s lymphoma cells. J. Virol. 2010; 84:13053-13058 (PMID:20943983).

Note: We recommend using the "Akata_inverted" genome and .bed and .gtf files for RNA-seq work. These are the most updated transcript annotations (as per O'Grady et al Nucleic Acids Res, above) and the genome configuration allows for the best representation of the LMP2A transcript which spans the terminal repeats.

EBV genome files for next generation sequence analysis

Fasta

".bed" annotation (Genome Viewer)

".ann" or ".gtf" annotation

(Transcript quantification)

B95-8/Raji

chrEBV(B95_8_Raji).fa

chrEBV(B95_8_Raji).bed

chrEBV(B95_8_Raji).ann

B95-8/Raji - Inverted

chrEBV(B95_8_Raji_Inverted).fa

chrEBV(B95_8_Raji_Inverted).bed

chrEBV(B95_8_Raji_Inverted).ann

Akata

chrEBV(Akata).fa

chrEBV(Akata).bed

Akata - Inverted

(updated 8/25/2016 - O'Grady et al)

chrEBV(Akata_Inverted).fa

chrEBV(Akata_Inverted).bed

chrEBV(Akata_Inverted).gtf

Mutu

chrEBV(Mutu).fa

chrEBV(Mutu).bed

AG876

chrEBV(AG876).fa

chrEBV(AG876).bed

chrEBV(AG876).ann

AG876 - Inverted

Type I

Type II