|
| Status |
Public on Jun 30, 2011 |
| Title |
MammaryTissue-24h-Saline-BiologicalRep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse left mammary gland tissue at 24hr post saline injection
|
| Organism |
Mus musculus |
| Characteristics |
Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: left-side mammary gland, Treatment: Saline injected, Time post-injection: 24hr
|
| Treatment protocol |
The tissue samples were stored in RNA Later (Ambion, Austin, TX).
|
| Growth protocol |
The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
|
| Scan protocol |
according to Affymetrix protocol
|
| Description |
gene expression data in mammary tissue sampled at 24 hr post saline injection
|
| Data processing |
For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
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| |
|
| Submission date |
Jan 21, 2009 |
| Last update date |
Jun 30, 2011 |
| Contact name |
Roger Luis Vallejo |
| E-mail(s) |
roger.vallejo@ars.usda.gov
|
| Phone |
304-724-8340
|
| Organization name |
USDA-ARS
|
| Department |
NCCCWA
|
| Street address |
11861 Leetown Rd.
|
| City |
Kearneysville |
| State/province |
WV |
| ZIP/Postal code |
25430 |
| Country |
USA |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE14485 |
Expression data from mouse model of Ecoli mastitis |
|
