|
| Status |
Public on Nov 16, 2011 |
| Title |
LNC Recovery, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
LEW rat Recovery
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Lymph node cell (LNC)
genotype: RT.1l
age: adult rats 5-6 week-old
strain: Lewis
disease state: recovery
|
| Treatment protocol |
Arthritis induction: Lewis rats, male, 5-6 wk, were immunized subcutaneously with heat-killed Mycobacterium tuberculosis H37Ra (Mtb) following standard procedure for adjuvant arthritis induction as described in our publications. Rats were observed for signs of arthritis..
Tolerance induction: Lewis rats were injected with Bhsp65 intraperitoneally (3 injections on alternate days) before arthritis induction, following standard procedure described in our publication.
LNC harvested from arthritic rats in incubation phase (preclinical arthritis) and those from tolerized rats were cultured in HL-1 medium in the presence or absence of Bhsp65 for 24 h. For ex vivo testing, LNC were not cultured in vitro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA mini-column was used to purify RNA obtained from Trizol isolation
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
cRNA was hybridized on affymetrix gene chip using GeneChip Fluidics Station 450.following manufacturer's instructions
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from LNC of rats 5-6 week-old
|
| Data processing |
Affymetrix.cel files were checked for quality and corrected for background using Affymetrix Expression Console™ 1.1. The data were normalized and the median polished using robust multi-array (RMA). Thereafter, Significance Analysis of Microarrays (SAM) was used to compare gene expression levels between two different groups by limiting the false discovery rate (FDR) to below 5%. Further analysis was performed using Uniprot, Gene Ontology (GO) and KEGG databases. The microarray experimental plan and data analysis are in accordance with MIAME guidelines.
|
| |
|
| Submission date |
Aug 10, 2011 |
| Last update date |
Nov 16, 2011 |
| Contact name |
Kamal D. Moudgil |
| E-mail(s) |
kmoud001@umaryland.edu
|
| Phone |
410-706-7804
|
| Fax |
410-706-2129
|
| Organization name |
University of Maryland School of Medicine
|
| Department |
Microbiology and Immunology
|
| Street address |
685 W. Baltimore Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE31314 |
Gene expression profile of preclinical arthritis and its modulation by antigen-induced tolerance |
|
