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Sample GSM949329 Query DataSets for GSM949329
Status Public on Feb 06, 2013
Title GRA16-dependent host transcriptional responses HFF infected with T. gondii [RH_WT]
Sample type RNA
Source name HFF infected with T. gondii RH_WT
Organism Homo sapiens
Characteristics host cell: Human foreskin fibroblast (HFF)
parasites: RH delta ku80 wild type
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 Cy3
Label protocol NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy3
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 18, 2012
Last update date Feb 06, 2013
Contact name Mohamed-ali HAKIMI
Phone (33)476637469
Organization name CNRS
Department UMR5309
Street address Domaine de la Merci, Campus Santé
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

Data table header descriptions
VALUE log2 value of normalized intensity of each group (averaged intensity of replicate samples)

Data table
AB000409 431.7987333
AB002294 833.2311
AB002308 8276.314667
AB002311 685.6431767
AB002313 4862.255667
AB002377 1671.6351
AB002381 870.4533233
AB002382 6661.348667
AB003177 2088.956067
AB003333 10243.32567
AB007457 5287.047833
AB007870 601.64866
AB007877 1823.900867
AB007895 451.1460367
AB007921 717.4842767
AB007923 929.7441433
AB007940 667.89605
AB010419 532.2845333
AB011088 5157.673133
AB011157 647.5058533

Total number of rows: 22175

Table truncated, full table size 455 Kbytes.

Supplementary file Size Download File type/resource
GSM949329_replicate1.txt.gz 2.3 Mb (ftp)(http) TXT
GSM949329_replicate2.txt.gz 2.3 Mb (ftp)(http) TXT
GSM949329_replicate3.txt.gz 2.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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