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Sample GSM947409 Query DataSets for GSM947409
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
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 629.0652667
AB002294 844.7409667
AB002308 6879.8511
AB002311 659.2680167
AB002313 7167.546433
AB002377 1322.5325
AB002381 1245.636767
AB002382 8561.296333
AB003177 2257.6909
AB003333 8807.521667
AB007457 5947.266167
AB007870 356.8247167
AB007877 1739.4717
AB007895 408.7294433
AB007921 791.5638867
AB007923 1050.4827
AB007940 572.4134233
AB010419 543.4790967
AB011088 4716.493767
AB011157 619.16272

Total number of rows: 22175

Table truncated, full table size 454 Kbytes.

Supplementary file Size Download File type/resource
GSM947409_replicate1.txt.gz 2.3 Mb (ftp)(http) TXT
GSM947409_replicate2.txt.gz 2.3 Mb (ftp)(http) TXT
GSM947409_replicate3.txt.gz 2.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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