|
| Status |
Public on Sep 01, 2015 |
| Title |
pancreas-wildtype-2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse pancreas obtained at baseline
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: Male
genotype: WT
|
| Treatment protocol |
Mice were untreated and uninfected.
|
| Growth protocol |
Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol except for adding output of raw array data for beadlevel analyses
|
| Description |
mouse pancreas gene expression, baseline, wild-type, C57BL/6J, male.
|
| Data processing |
Hybridization and scanning of BeadChip arrays was performed according to the manufacturer's instructions, using BeadStudio 3.0 software (Illumina). In order to perform bead-level analysis, raw data is exported from BeadStudio. Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw bead-level intensity data was imported using functions from the beadarray package, including background correction. Each array consists of two strips. Due to potential variation in the data from the two different strips (see Shi et al. (2009) [PMID:19903361]), we treated the individual strips from each sample separately. Thus, for each strip, low-level analysis and quality control was performed using functions from the beadarray package (see Ritchie et al. (2011) [PMID:22144879]). The BASH algorithm was then applied to the raw data to mask beads affected by large spatial artifacts, followed by bead-type summarization, including removal of outlier beads. Summarized data were Log2-transformed, followed by quantile normalization.
|
| |
|
| Submission date |
Sep 15, 2014 |
| Last update date |
Sep 01, 2015 |
| Contact name |
Anand Champak Patel |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pulmonary/Critical Care Medicine
|
| Lab |
Patel
|
| Street address |
Campus Box 8116, 660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL6481 |
| Series (2) |
| GSE61414 |
Pancreatic Gene Expression from Wild-Type, Stat1-Transgenic, and Stat1-CC-Transgenic Mice |
| GSE61421 |
PARP9 and DTX3L in Antiviral Host Defense |
|
