|
| Status |
Public on Jan 01, 2011 |
| Title |
D4-1 |
| Sample type |
RNA |
| |
|
| Source name |
Division 4
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
tissue: lymph node
cell type: DO11.10 CD4 T effectors divided 3 times
|
| Growth protocol |
CFSE-labeled DO11.10 CD4 naïve T cells were transferred into Balb/c mice and the hosts were immunized with OVA peptide in CFA. 66-72 hrs later, the lymph node cells were harvested and Divisions 3, 4, 6 and 8 were sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using TRI reagent (Sigma Aldrich)
|
| Label |
Cy3
|
| Label protocol |
Total RNA was used to make the biotin-labeled antisense RNA target using the Illumina TotalPrep RNA amplification kit by following the manufacturer`s procedures.
|
| |
|
| Hybridization protocol |
Antisense RNA was hybridized to Illumina beadchip array at 58C for 20hrs. After hybridization, the chips were washed and stained with streptavidin-Cy3.
|
| Scan protocol |
The image data was acquired by BeadArray reader (Illumina)
|
| Description |
Division 4 (experiment 1)
|
| Data processing |
The microarray data was processed by using BeadStudio v2.0 software, background substracted, and normalized using cubic spline algorithm. Genes with Detection p-val less than 0.05 were included. Genes differentially expressed between groups were identified using the Illumina custom error model implemented in BeadStudio. Division 4 (D4) was set as control group. Genes were considered significantly differentially expressed when p values were less than 0.05 (Diffscore 13) and the fold change was greater than 1.8 between D4 and D8 groups.
|
| |
|
| Submission date |
Nov 04, 2010 |
| Last update date |
Jan 01, 2011 |
| Contact name |
Betul Fatma Guloglu |
| E-mail(s) |
guloglub@health.missouri.edu
|
| Phone |
5735291272
|
| Organization name |
University of Missouri
|
| Department |
Microbiology and Immunology
|
| Lab |
Habib Zaghouani
|
| Street address |
1 Hospital Drive, M616 Medical Sciences Building
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE25141 |
Comparison of genes differentially expressed among effectors with high and low memory potential |
|
