|
| Status |
Public on May 15, 2014 |
| Title |
WT Un 1 |
| Sample type |
RNA |
| |
|
| Source name |
WT BMDM untreated
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
age: 6 week
strain: C57Bl/6
treatment: untreated
|
| Treatment protocol |
Cells were untreated (plain media) or treated with 10ng/ml LPS or 1ng/ml TNFa for 4 hours in differentiation media (DMEM + pen/strep + 10% FBS + 10% L929 supernatant).
|
| Growth protocol |
Bone marrow was collected from 6 week old male mice and plated at a density of 2x10^7 per 10cm dish. One dish was used for each sample. Differentiated with 10% L929 supernatant for 1 week with media changes every 3 days. The experiment was performed on day 7 of differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by a QIAeasy kit (QIAgen) and analyzed for integrity by agarose gel
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeling of RNA was done by standard protocol.
|
| |
|
| Hybridization protocol |
Hybridization was done by standard protocol.
|
| Scan protocol |
Slides were scanned by standard protocol on an Agilent scanner.
|
| Description |
Gene expression
|
| Data processing |
Data were analyzed using Partek Genomics Suite 6.4. We used the RMA algorithm for data normalization. Thresholds for selecting significant genes were set at >= 2-fold and FDR p<0.05. Genes met both criteria simultaneously were considered as significant changes.
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
May 15, 2014 |
| Contact name |
Mary A Rodgers |
| Phone |
323-442-1066
|
| Organization name |
University of Southern California
|
| Department |
Molecular Microbiology and Immunology
|
| Lab |
Dr Jae Jung
|
| Street address |
1450 Biggy St, NRT 5517
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE57180 |
Global transcriptional profiles of WT and HOIL-1L-/- BMDMs in response to LPS and TNFa |
|
