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Sample GSM1015440 Query DataSets for GSM1015440
Status Public on Apr 23, 2013
Title IRF3/5/7 TKO 5b
Sample type RNA
 
Source name RPMI + rmGM-CSF purified BM-DC populations, mock and WNV infected with insect derived virus and RNA isolated 24 hours post infection.
Organism Mus musculus
Characteristics subject: Mouse_15
genotype: IRF3/5/7 TKO
cell type: bone marrow derived myeloid DC bmDCs
infection: mock
time point: 24 hours
Treatment protocol GM-CSF was replenished after 2 days and non-adherent cells were sub-cultured after 4 days. Sub-cultured cells were infected at an MOI of 25 with WNV-NY. To determine the percentage of cells infected, mDC were detached 24 h after WNV inoculation. Non-specific binding of antibody to Fc-γR was blocked with anti-CD16/CD32 (Biolegend), and all subsequent surface staining (I-Ab-FITC, CD86-PE, and CD11c-APC (all from Biolegend)) was performed in PBS supplemented with 2% fetal calf serum. Cells were fixed, permeabilized, and then stained with Alexa-647 conjugated anti-WNV E16 anti-WNV MAb. For microarray analysis, total RNA was harvested at 24 hours post-infection.
Growth protocol Bone marrow was cultured in RPMI supplemented with 10% fetal bovine serum, penicillin/streptomycin, L-glutamine, non-essential amino acids, 55 μM β-mercaptoethanol and 20 ng/ml recombinant mouse GM-CSF (eBioscience) for 6 days in non-tissue culture treated plates.
Extracted molecule total RNA
Extraction protocol The DC/Mac populations were harvested at each desired post-infection time point. The cells were washed once with RT 1XPBS (about 2ml/Well). Then 0.5ml added of warmed trypsin to each well, incubate 10 min at 37°C. Once this was done, 5 ml added of cold PBS w/ 10% serum or use 10% complete medium. The cells were then collected in 15ml conical tube. Cells were spun down at 1000-1200 RPM x 5 minutes at 4°C.
Label Biotin
Label protocol The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.
 
Hybridization protocol Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V2 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol
Scan protocol The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).
Description bmDC from Mouse_15, mock infected
Data processing Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation
 
Submission date Oct 04, 2012
Last update date Apr 23, 2013
Contact name Peter A Wilkinson
Organization name Case Western Reserve University
Department Pathology / Systems Biology & Bioinformatics
Street address 2103 Cornell Road
City Cleveland
State/province Ohio
ZIP/Postal code 44120
Country USA
 
Platform ID GPL6885
Series (1)
GSE41355 IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling

Data table header descriptions
ID_REF
VALUE Quantile normalized, log2 transformed intensities

Data table
ID_REF VALUE
ILMN_1250052 7.310226925
ILMN_3122480 6.772174495
ILMN_2599935 8.376268757
ILMN_2675543 6.871527527
ILMN_2686883 7.626604435
ILMN_2751818 6.90075291
ILMN_2728634 7.214594051
ILMN_3040515 6.843476685
ILMN_2711608 6.829064503
ILMN_1232875 7.636145786
ILMN_1258507 6.983961574
ILMN_2746142 6.74375476
ILMN_1252690 7.121484646
ILMN_2655499 6.871527527
ILMN_1252870 6.829064503
ILMN_1248179 6.785807141
ILMN_2649955 7.574861247
ILMN_2628708 7.864419779
ILMN_3024781 6.79980089
ILMN_2705628 11.39859246

Total number of rows: 25697

Table truncated, full table size 623 Kbytes.




Supplementary file Size Download File type/resource
GSM1015440_6197801007_E_beadTypeFile.txt.gz 167.5 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Raw data are available on Series record

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