Rene Warren 7 October 2011 SYNOPSIS -------- 75nt paired-end RNA-seq data from DLBCL patient cohort mined for presence of putative infectious agents. Microbial agent discovery performed as described in Moore et al. 2011 ACCESS TO THE DATA ------------------ Download DLBCL-EBV.tar.gz gunzip DLBCL-EBV.tar.gz tar -xvf DLBCL-EBV.tar REFERENCES ---------- Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, et al. 2011 The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue. PLoS ONE 6(5): e19838. doi:10.1371/journal.pone.0019838 Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. 2011. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 476:298-303. DATABASE -------- GENBANK refseq& complete microbial+viral genomes + HMP bacterial reference strains used for mining the NGS data set. The only HHV4 accessions in our sequence database are: gi|9629732|ref|NC_001844.1| Equid herpesvirus 4, complete genome gi|82503188|ref|NC_007605.1| Human herpesvirus 4 type 1, complete genome gi|13095578|ref|NC_002665.1| Bovine herpesvirus 4, complete genome gi|139424470|ref|NC_009334.1| Human herpesvirus 4, complete genome gi|146261990|ref|NC_001826.2| Murid herpesvirus 4, complete genome gi|51518014|ref|NC_006146.1| Macacine herpesvirus 4, complete genome gi|6625567|gb|AF105037.1| Murid herpesvirus 4 complete genome gi|84519641|gb|AY961628.3| Human herpesvirus 4 strain GD1, complete genome Thus, additional alignments are required to narrow down on the subtype. Sam files are provided such that NGS reads can be extracted and re-aligned to strains of interest. EBV (HHV4) FINDINGS ------------------- We found 4 DLBCL RNA-seq libraries with pair count >=10 aligning unambiguously to HHV4. Below are the Genbank accessions and description of each. gi|82503188|ref|NC_007605.1|,Human herpesvirus 4 type 1 complete genome gi|139424470|ref|NC_009334.1|,Human herpesvirus 4 complete genome gi|84519641|gb|AY961628.3|,Human herpesvirus 4 strain GD1 complete genome FILES ----- We are providing, for each of the 4 EBV positive library, a sam file that can easily be manipulated with samtools, to extract sequence alignments, quality scores and other NGS information. HS0649_HHV4.sam HS2051_HHV4.sam HS2056_HHV4.sam HS2937_HHV4.sam