|
| Status |
Public on Sep 21, 2013 |
| Title |
spleen_Myd88_PcAS_24h_3 |
| Sample type |
RNA |
| |
|
| Source name |
Myd88 knockout, whole spleen, P. chabaudi infection, 24h
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
background strain: C57BL/6
genotype/variation: Myd88 knockout
tissue: spleen
infection: P. chabaudi
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: Myd88PcAS-3
|
| 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 |
|
