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Sample GSM949319 Query DataSets for GSM949319
Status Public on Feb 06, 2013
Title Host transcriptional responses in mouse BMDM infected with T. gondii [Pru_WT]
Sample type RNA
 
Source name mouse BMDM infected with T. gondii Pru_WT
Organism Mus musculus
Characteristics strain: C57BL/6
host cell: Mouse bone marrow-derived macrophages (BMDM)
parasites: Prugniaud delta ku80 wild type
time point: 18 h post-infection
Treatment protocol Mouse BMDM were infected with Toxoplasma gondii tachyzoites (prepared from infected HFFs and washed in PBS) of the indicated strain at multiplicity of infection ~3; 18 hours post-infection, adherent cells and cells in the supernatent were harvested and lysed in Trizol reagent for RNA extraction.
Growth protocol Bone marrow-derived macrophages were obtained from 8-10-week old C57BL/6 mice purchased from JANVIER (France). Bone marrow
was isolated by flushing hind tibias and femurs using a 25-gauge needle and DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin. ~5 x 10^6 cells were resuspended in DMEM supplemented with 20 ng/mL M-CSF (Invitrogen)and plated in 10-cm nontissue culture-treated dishes (Corning). Cells were incubated at 37°C, with 5% CO2 in humidified air for 6 days. Adherent cells were harvested in cold-PBS(4°C) using a cell scraper, and replated at 8 x 10e6 cells per 10-cm2 plate for the assay.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy3
Label protocol NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy3
 
Hybridization protocol The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies).
Scan protocol After washing, slides were scanned with the Agilent DNA microarray Scanner. Data was extracted and normalized using Agilent Feature Extraction Software (version 11.0.1.1).
Description Gene expression data from BMDM infected with indicated T. gondii strain, 18 h post-infection
Data processing Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 9 samples have flags in Detected or Not Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.
 
Submission date Jun 18, 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 GPL11202
Series (2)
GSE38779 Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression
GSE38782 A Toxoplasma dense granule protein, GRA24, modulates the early immune response to infection by promoting a direct and sustained host p38 MAPK activation

Data table header descriptions
ID_REF
VALUE log2 value of normalized intensity of each group (averaged intensity of replicate samples)
Mean(RawData_PRU_WT) Raw Intensity of each group (averaged intensity of replicate samples)

Data table
ID_REF VALUE Mean(RawData_PRU_WT)
A_55_P1989846 8.431758 235.32861
A_55_P2022211 11.962814 3934.28
A_55_P1980764 3.9314766 13.664871
A_55_P1964375 9.887089 692.81464
A_51_P128876 13.445245 9245.412
A_52_P219230 5.1444407 39.44112
A_51_P207591 5.4488378 31.582026
A_55_P2131920 5.655752 44.590008
A_55_P2404223 6.5606008 71.42927
A_55_P2101944 12.634625 5752.9487
A_52_P358860 5.460356 87.07438
A_51_P119031 7.710942 140.21527
A_51_P343900 9.594069 623.18994
A_51_P487813 11.142853 1923.1344
A_52_P613977 9.965649 737.6939
A_55_P2052210 13.869202 13504.12
A_51_P128987 10.146674 925.27997
A_51_P111223 4.7852454 22.266253
A_55_P1958431 5.214472 29.705175
A_55_P2111153 10.110538 804.66864

Total number of rows: 24736

Table truncated, full table size 791 Kbytes.




Supplementary file Size Download File type/resource
GSM949319_replicate1.txt.gz 2.2 Mb (ftp)(http) TXT
GSM949319_replicate2.txt.gz 2.2 Mb (ftp)(http) TXT
GSM949319_replicate3.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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