Virus Expression Database
Submitted by Winnie Liang (Translational Genomics, USA) on Apr 22 2008
Platform: microarray – [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Pubmed: None listed
Summary Smallpox is a highly communicable, often fatal diseae. There is currently no licensed treatment for smallpox and vaccinia virus (VV) is currently used for immunization. While immunization with VV can provide good protection against exposure to the smallpox virus, the current vaccine is far from optimal. Complications occur in 1/1,000-1/10,000 vaccinees, with at least one death per million vaccinees. We have constructed recombinant VV strains which are less pathogenic, yet provide a protective immune response. These viruses contain various mutations in the E3L which is known to block the host antiviral response. Identifying the host genes involved in producing a strong protective immunological response to these attenuated viruses would not only increase our understanding of the proteins and pathways involved in effective smallpox vaccination, but aid in the development of alternative vaccine strains which enhance these specific immune responses.
We will determine gene expression patterns in HeLa cells at various times following infection with wtVV and several VV constructs containing mutations in the E3L gene.
The VV E3L gene product blocks the host antiviral response by sequestering viral danger signals, including double-stranded RNA and Z-DNA. VV constructs containing mutations in E3L which allow host cell recognition of either of these danger signals leads to a decrease in viral pathogensis. In this project we will dissect the cellular inflammatory response to infection with wtVV in comparison to VV containing mutations in the E3L gene. By understanding why certain strains of VV are non-pathogenic, yet highly immunogenic, it is possible to gain a better understanding on the mechanisms of poxvirus pathogenesis and the host response.
We will examine three times points following infection with VV: 2 HPI, 6 HPI and 9 HPI. These times points represent keys points in the virus replication cycle. Several VV constructs will be used which contain mutations in the E3L gene. These constructs alter the ability of E3L to sequester double-stranded RNA and/or Z-DNA and therefore have a direct effect on viral pathogenesis. Fourteen constructs will be used including: mock, wtVV, VVdelE3L, VVE3Ldel83N, VVE3Ldel37N, VVE3Ldel26C, VVE3Ldel7C, VVE3L Y48A, VVE3L P63A, VVE3L K167T, VV-ATV, VV-ADAR/E3L, VVdelK3L, VVdelK3L-E3Ldel37N. Cells will be infected at an MOI of 5 to allow infection of all cells. At each time point, cells will be harvested by scraping. RNA will be isolated using a Trizol RNA extraction protocol (Invitrogen) followed by RNA purification using the RNeasy cleanup kit available from Qiagen.
Keywords: time-course
| ID | Title | Cell Type | Timepoint | Reported Virus | Virus Species | Exclusion Reason |
|---|---|---|---|---|---|---|
| GSM283458 | HeLa Cell Line, unknown: wtVV, 2 HPI | cervical adenocarcinoma cell line  [HeLa  ] |
2 hrs | VV | Vaccinia virus | |
| GSM283459 | HeLa Cell Line, unknown: wtVV, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | |
| GSM283460 | HeLa Cell Line, unknown: wtVV, 9HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | |
| GSM283461 | HeLa Cell Line, unknown: VVdelE3L, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283462 | HeLa Cell Line, unknown: VVdelE3L, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283463 | HeLa Cell Line, unknown: VVdelE3L, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283464 | HeLa Cell Line, unknown: VVE3Ldel83N, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283465 | HeLa Cell Line, unknown: VVE3Ldel83N, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283466 | HeLa Cell Line, unknown: VVE3Ldel83N, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283467 | HeLa Cell Line, unknown: VVE3Ldel26C, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283468 | HeLa Cell Line, unknown: VVE3Ldel26C, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283469 | HeLa Cell Line, unknown: VVE3Ldel26C, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283470 | HeLa Cell Line, unknown: VVE3Ldel7C, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283471 | HeLa Cell Line, unknown: VVE3Ldel7C, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283472 | HeLa Cell Line, unknown: VVE3Ldel7C, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283473 | HeLa Cell Line, unknown: VVE3L Y48A, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283474 | HeLa Cell Line, unknown: VVE3L Y48A, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283475 | HeLa Cell Line, unknown: VVE3L Y48A, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283476 | HeLa Cell Line, unknown: VVE3L Y48F, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283477 | HeLa Cell Line, unknown: VVE3L Y48F, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283478 | HeLa Cell Line, unknown: VVE3L Y48F, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283479 | HeLa Cell Line, unknown: VV-ATV, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283480 | HeLa Cell Line, unknown: VV-ATV, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283481 | HeLa Cell Line, unknown: VV-ATV, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283482 | HeLa Cell Line, unknown: VV-ADAR/E3L, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283483 | HeLa Cell Line, unknown: VV-ADAR/E3L, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283484 | HeLa Cell Line, unknown: VV-ADAR/E3L, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283485 | HeLa Cell Line, unknown: VVdel37N, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283486 | HeLa Cell Line, unknown: VVdel37N, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283487 | HeLa Cell Line, unknown: VVdel37N, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283488 | HeLa Cell Line, unknown: VVdelK3L, 2 HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283489 | HeLa Cell Line, unknown: VVdelK3L, 6 HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283490 | HeLa Cell Line, unknown: VVdelK3L, 9 HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283491 | HeLa Cell Line, unknown: VVdelK3Ldel37N, 2HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283492 | HeLa Cell Line, unknown: VVdelK3Ldel37N, 6HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283493 | HeLa Cell Line, unknown: VVdelK3Ldel37N, 9HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | VV | Vaccinia virus | Extra interventions mutated to avoid response |
| GSM283494 | HeLa Cell Line, unknown: mock infected 6HPI | cervical adenocarcinoma cell line [HeLa ] |
2 hrs | mock | Uninfected | |
| GSM283495 | HeLa Cell Line, unknown: mock infected 2HPI | cervical adenocarcinoma cell line [HeLa ] |
6 hrs | mock | Uninfected | |
| GSM283496 | HeLa Cell Line, unknown: mock infected 9HPI | cervical adenocarcinoma cell line [HeLa ] |
9 hrs | mock | Uninfected |