|
| Status |
Public on Jan 06, 2015 |
| Title |
Chronic Pg 1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse aortic tissue, collected 9 weeks after the end of P. gingivalis administration.
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: aortic tissue
timepoint: chronic
treatment: P. gingivalis
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TriZol extraction reagent (Invitrogen) using TissueLyser II in pre-cooled blocks (Qiagen). RNA was further purified using the RNAeasy kit (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from mouse aortic tissue, collected 9 weeks after the end of P. gingivalis administration.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).
|
| |
|
| Submission date |
Aug 05, 2014 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL13730 |
| Series (1) |
| GSE60086 |
Distinct gene signatures define pathogen- versus diet-induced atherosclerosis development |
|
