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Sample GSM1018267 Query DataSets for GSM1018267
Status Public on Sep 21, 2013
Title spleen_Unc93b1_mock_4
Sample type RNA
 
Source name Unc93b1-3d, whole spleen, mock infection, 24h
Organism Mus musculus
Characteristics gender: female
background strain: C57BL/6
genotype/variation: Unc93b1 knockout
tissue: spleen
infection: mock
infection duration: 24h
Treatment protocol Mice were either injected ip with 10^6 uninfected or infected erythrocytes from a donor mouse
Growth protocol Total spleen RNA extraction 24h post mock- or P. chabaudi-infection
Extracted molecule total RNA
Extraction protocol RNA was isolated from frozen spleens disrupted in 1mL Trizol at 30/s for 3 min in a TissueLyser II (Qiagen, Valencia, CA), followed by RNA isolation (RNAqueous Micro, Life Technologies). Purified RNA was amplified (MessageAmp II , Life Technologies) with minor modifications to manufacturer’s instructions to generate amino-allyl incorporated amplified RNA.
Label Cy3
Label protocol 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns
 
Hybridization protocol 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent) as per manufacturers protocol.
Scan protocol Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff
Description Sample name: Uncmock-4
Data processing Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization. Control features and sample features with saturated, non-uniform feature, and non-uniform background flags were removed. Genes present across 70% of arrays were retained, log2 transformed, KNN-imputed, and quantile normalized. Genes determined to be not expressed were filtered out (expressed genes = log2 intensity >= 7 across all samples within a group). Arrays were median centered, followed by median centering of genes.
 
Submission date Oct 11, 2012
Last update date Sep 22, 2013
Contact name Charlie Kim
E-mail(s) cckim47@gmail.com
Organization name University of California, San Francisco
Department Medicine
Lab Kim
Street address 1001 Potrero Ave
City San Francisco
State/province CA
ZIP/Postal code 94110
Country USA
 
Platform ID GPL13912
Series (1)
GSE41496 Toll-like receptor 7 is a primary sensor of malaria infection

Data table header descriptions
ID_REF
VALUE Quantile normalized log2 Cy3 intensity, gene-centered

Data table
ID_REF VALUE
13 -0.635075677
14 -0.003479772
17 0.746457825
19 0.138572845
20 0.23071028
22 1.595700488
23 0.536805758
29 -0.062074444
30 -0.750101184
31 -0.107042315
33 0.40707577
37 -1.914839252
40 0.766020327
42 0.370045035
48 0.688174933
49 -0.328005403
50 -0.050411687
55 0.308975936
57 0.484254666
59 0.002922387

Total number of rows: 20688

Table truncated, full table size 365 Kbytes.




Supplementary file Size Download File type/resource
GSM1018267_252800513388_S01_GE1-v1_95_Feb07_2_4.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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