NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1018275 Query DataSets for GSM1018275
Status Public on Sep 21, 2013
Title spleen_Myd88_mock_4
Sample type RNA
 
Source name Myd88 knockout, whole spleen, mock infection, 24h
Organism Mus musculus
Characteristics gender: female
background strain: C57BL/6
genotype/variation: Myd88 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: Myd88mock-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 0.732071468
14 0.155196493
17 -0.08712961
19 -0.04741504
20 -0.351358625
22 -0.500177943
23 -0.013370888
29 -0.567824003
30 -0.314127623
31 0.17560607
33 -0.120910415
37 0.135596978
40 0.012540152
42 -0.13583922
48 0.499053108
49 0.115510563
50 -0.001547683
55 -0.071639276
57 0.008199146
59 0.170206935

Total number of rows: 20688

Table truncated, full table size 365 Kbytes.




Supplementary file Size Download File type/resource
GSM1018275_252800513391_S01_GE1-v1_95_Feb07_2_4.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap