|
| Status |
Public on Feb 15, 2019 |
| Title |
HA_WT_mean |
| Sample type |
RNA |
| |
|
| Source name |
HA infected with Pruku80 (WT), mean of replicate 1,2 and 3
|
| Organism |
Homo sapiens |
| Characteristics |
host cell: Human primary Astrocyte (HA)
infection: Pruku80 (WT)
tg type strain: Type II
|
| Treatment protocol |
Host cells were left uninfected or infected for 24 hours with Toxoplasma type II strains.
|
| Growth protocol |
T. gondii strains were maintained in vitro by serial passage on monolayers of HFFs. HFF and HA human primary cells were cultured in DMEM supplemented with 10% heat inactivated FBS (Invitrogen), 10 mM Hepes buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
Gene expression
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 27 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the R software (version 2.15). GO analysis and Pathway analysis were performed in the standard enrichment computation method.
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
Feb 15, 2019 |
| 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 |
GPL13497 |
| Series (2) |
| GSE113618 |
The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2 |
| GSE113658 |
The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2 |
|
