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Status |
Public on Sep 21, 2013 |
Title |
spleen_B6_mock_4 |
Sample type |
RNA |
|
|
Source name |
C57BL/6, whole spleen, mock infection, 24h
|
Organism |
Mus musculus |
Characteristics |
gender: female background strain: C57BL/6 genotype/variation: wildtype 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
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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: B6mock-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.
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|
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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 |
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