|
| Status |
Public on Mar 04, 2015 |
| Title |
Ifnar1-/- BMDM infected with Francisella, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow-derived macrophages infected for 8 hour with Francisella novicida, Ifnar1-/-
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Ifnar1-/-
cell type: bone marrow-derived macrophages
treatment: infected with Francisella novicida strain U112 for 8 hours
|
| Treatment protocol |
BMDMs in antibiotic-free medium were seeded onto 12-well plates at a density of 1 x 10^6 cells per well, followed by incubation overnight. Cells were then infected at an MOI of 100 with Francisella novicida strain U112 and cultured for an additional 8 hours before extracting total RNA.
|
| Growth protocol |
Primary BMDMs were grown for 5-6 days in IMDM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma). F. novicida strain U112 was grown overnight under aerobic conditions at 37 °C in BBL Trypticase Soy Broth (211768; BD) supplemented with 0.2% l-cysteine (Fisher).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy protocol according to the manufacturer's recommended methods.
|
| Label |
biotin
|
| Label protocol |
Sense target cDNA was prepared from 200ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).
|
| |
|
| Hybridization protocol |
Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
SMM008
Ifnar1-/- mouse backcrossed to the C57BL/6 background.
|
| Data processing |
Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.
|
| |
|
| Submission date |
Mar 03, 2015 |
| Last update date |
Mar 04, 2015 |
| Contact name |
Geoffrey Neale |
| E-mail(s) |
[email protected]
|
| Organization name |
St Jude Childrens Research Hospital
|
| Department |
Hartwell Center
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE66461 |
The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection |
|
