|
| Status |
Public on Feb 06, 2013 |
| Title |
GRA16-dependent host transcriptional responses HFF infected with T. gondii [RH_GRA16-KO] |
| Sample type |
RNA |
| |
|
| Source name |
HFF infected with T. gondii RH_GRA16-KO
|
| Organism |
Homo sapiens |
| Characteristics |
host cell: Human foreskin fibroblasts (HFF)
parasite: RHku80(deltaGRA16) mutant
time point: 21 h post-infection
|
| Treatment protocol |
HFFs were infected with Toxoplasma gondii tachyzoites (prepared from infected HFFs and washed in PBS) of the indicated strain at multiplicity of infection ~3; 21 hours post-infection, infected cells were washed in PBS before being harvested using a cell scraper and lysed in Trizol reagent for RNA extraction.
|
| Growth protocol |
HFFs were grown in DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin and incubated at 37°C, with 5% CO2 in humidified air for 6-10 days. ~5 x 10e6 confluent monolayer of cells were washed and incubated in growth media in the absence of serum for 5 hours. Serum starved cells were used for the assay.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy5
|
| |
|
| Hybridization protocol |
standard protocol
|
| Scan protocol |
After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 software.
|
| Description |
Gene expression data from HFFs infected with indicated T. gondii strain, 21 h post-infection
|
| Data processing |
Raw signal intensities were normalized in RMA method by NimbleScan v2.5, and low intensity genes were filtered (Genes that Intensity at least 6 out of 6 samples have values >= lower cut-off: 300.0 were chosen for further analysis).
|
| |
|
| Submission date |
Jun 13, 2012 |
| Last update date |
Feb 06, 2013 |
| Contact name |
Mohamed-ali HAKIMI |
| E-mail(s) |
mohamed-ali.hakimi@univ-grenoble-alpes.fr
|
| Phone |
(33)476637469
|
| Organization name |
CNRS
|
| Department |
UMR5309
|
| Lab |
IAB - HAKIMI Team
|
| Street address |
Domaine de la Merci, Campus Santé
|
| City |
LA TRONCHE |
| State/province |
Grenoble |
| ZIP/Postal code |
38700 |
| Country |
France |
| |
|
| Platform ID |
GPL10191 |
| Series (1) |
| GSE38779 |
Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression |
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