 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 01, 2012 |
| Title |
H1N1 influenza A/New Caledonia/20/1999 time series in monocyte-derived dendritic cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs) infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999. To provide a mechanistic explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a statistically rigorous enrichment approach integrating genome-wide expression kinetics and time-dependent promoter analysis. Our approach, TI me-Dependent Activity Linker (TIDAL), generates a regulatory network that connects transcription factors associated with each temporal phase of the response into a coherent linked cascade. TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to influenza. To demonstrate the generality of this approach, TIDAL was also used to generate a network for the DC response to measles infection.
|
| |
|
| Overall design |
Monocyte-derived DCs were obtained from healthy human blood donors following a standard protocol. The recent seasonal H1N1 influenza virus A/New Caledonia/20/1999 (NC) virus was titrated by immunofluorescence 18 hours after infection of MDCK cell plates using monoclonal antibodies specific for Influenza-NP protein generated by the Mount Sinai Hybridoma Core Facility followed by addition of anti-mouse IgG-FITC and visualization using fluorescent microscopy. For infection of naive DCs, NC stocks were appropriately diluted in Dulbecco’s Modified Eagle Medium (DMEM) and added directly into pelleted DCs at a multiplicity of infection (MOI) of 1 After incubation for 40 minutes at 37 ◦C, fresh DC growth medium (without GMCSF and IL-4) was added back to the infected cells (1 106 cells/ml) for the remainder of the infection. The reaction was stopped at 1, 2, 4, 6, 8, 10, and 12 hours after infection by fixing the cells with RNAprotect Cell Reagent (Qiagen, Duesseldorf Germany). Naive non-infected DCs underwent the same experimental procedure as infected DCs in the absence of virus to ensure that mechanical manipulations could not be responsible for differences in experimental readouts. All time points and controls were performed in triplicates. Cells were homogenized by using QIAshredder microcentrifuge spin-columns (Qiagen, Duesseldorf Germany) and RNA was isolated from cells using Qiagen Micro RNeasy plus kit following the manufactures protocol (Qiagen, Duesseldorf Germany). RNA quality was assayed by determination of the RNA integrity number using the 2100 Bioanalyzer (Agilent). RNA samples were processed and hybridized to HumanHT-12 v4 Expression BeadChip Kit (Illumina San Diego, CA) by the Mount Sinai Genomics Institute following the manufacturer’s instructions, and raw expression data were output by the Illumina GenomeStudio software.
|
| |
|
| Contributor(s) |
Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Sep 21, 2012 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Juilee Thakar |
| E-mail(s) |
[email protected]
|
| URL |
http://medicine.yale.edu/pathology/people/juilee_thakar.profile
|
| Organization name |
Yale medical school
|
| Department |
Pathology
|
| Lab |
Kleinstein
|
| Street address |
300 George street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
|
| Samples (24)
|
| GSM1008157 |
Four hour after the infection replicate 1 |
| GSM1008158 |
Six hour after the infection replicate 1 |
| GSM1008159 |
Eight hour after the infection replicate 1 |
| GSM1008160 |
Ten hour after the infection replicate 1 |
| GSM1008161 |
Twelve hour after the infection replicate 1 |
| GSM1008162 |
control replicate 2 |
| GSM1008163 |
One hour after the infection replicate 2 |
| GSM1008164 |
Two hour after the infection replicate 2 |
| GSM1008165 |
Four hour after the infection replicate 2 |
| GSM1008166 |
Six hour after the infection replicate 2 |
| GSM1008167 |
Eight hour after the infection replicate 2 |
| GSM1008168 |
Ten hour after the infection replicate 2 |
| GSM1008169 |
Twelve hour after the infection replicate 2 |
| GSM1008170 |
control replicate 3 |
| GSM1008171 |
One hour after the infection replicate 3 |
| GSM1008172 |
Two hour after the infection replicate 3 |
| GSM1008173 |
Four hour after the infection replicate 3 |
| GSM1008174 |
Six hour after the infection replicate 3 |
| GSM1008175 |
Eight hour after the infection replicate 3 |
| GSM1008176 |
Ten hour after the infection replicate 3 |
| GSM1008177 |
Twelve hour after the infection replicate 3 |
|
| Relations |
| BioProject |
PRJNA175663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41067_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| GSE41067_non-normalized.txt.gz |
6.9 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...