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Sample GSM945860 Query DataSets for GSM945860
Status Public on Feb 06, 2013
Title GRA16-dependent host transcriptional responses in mouse BMDM infected with T. gondii [RH_GRA16-KO]
Sample type RNA
 
Source name mouse BMDM infected with T. gondii RH_GRA16-KO
Organism Mus musculus
Characteristics strain: C57BL/6
host cell: Mouse bone marrow-derived macrophages (BMDM)
parasite: RHku80(deltaGRA16) mutant
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 Cy5
Label protocol NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy5
 
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 08, 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 (1)
GSE38779 Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression

Data table header descriptions
ID_REF
VALUE log2 value of normalized intensity of each group (averaged intensity of replicate samples)
Mean(RawData_RH_GRA16_KO) Raw Intensity of each group (averaged intensity of replicate samples)

Data table
ID_REF VALUE Mean(RawData_RH_GRA16_KO)
A_55_P1989846 9.637506 726.8198
A_55_P2022211 12.778195 6760.109
A_55_P1980764 5.8870277 53.675106
A_55_P1964375 10.866473 1739.52
A_51_P128876 13.6295805 12361.817
A_52_P219230 6.7830734 98.22532
A_51_P207591 5.945843 54.658478
A_55_P2131920 7.7172027 186.56255
A_55_P2404223 7.113607 122.33718
A_55_P2101944 12.551178 5747.373
A_52_P358860 8.841676 419.986
A_51_P119031 9.823411 827.69556
A_51_P343900 10.834115 1707.605
A_51_P234359 5.4672914 40.367363
A_51_P487813 12.089444 4159.6475
A_52_P613977 11.075676 2012.7584
A_55_P2052210 15.276149 39131.76
A_51_P128987 10.938008 1823.7001
A_51_P111223 6.2348 90.50939
A_55_P1958431 6.3522053 75.262245

Total number of rows: 28868

Table truncated, full table size 923 Kbytes.




Supplementary file Size Download File type/resource
GSM945860_replicate1.txt.gz 2.1 Mb (ftp)(http) TXT
GSM945860_replicate2.txt.gz 2.1 Mb (ftp)(http) TXT
GSM945860_replicate3.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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