|
| Status |
Public on Nov 30, 2017 |
| Title |
WT BMDC matured only, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
WT BMDC, no antigen
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129Sv/Ev
genotype/variation: WT
cell type: Bone marrow-derived dendritic cells (BMDCs)
antigen: None
|
| Treatment protocol |
Mouse BMDCs were unloaded or loaded with 10ug/mL endo-free OVA protein and 10ug/mL SIINFEKL peptide for 3 hours in 5% serum media. Cells were matured with cytokine cocktail (10ng/mL TNFa, 15ng/mL IL-6, 10ng/mL IL-1b, 1ug/mL PGE2) for 48hours prior to harvest.
|
| Growth protocol |
Mouse BMDCs were ex vivo differentiated with 20ng/mL GM-CSF and 10ng/mL IL-4 for 6 days prior to treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The concentration of total RNA was assessed using the Nanodrop ND-1000 Spectrophotometer (ThermofisherScientific). Once the sample concentration was determined, the integrity of the total RNA was assessed using the Agilent 2100 Bioanalyzer Nanokit. Samples with a minimum concentration of 33 ng/ul were selected for target preparation using the WT Plus assay (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA was used to process the samples for Whole Transcriptome Expression Analysis with the WT Plus reagent kit (Affymetrix). Samples were reversed transcribed to generate amplified, fragmented and biotinylated sense-strand cDNA, according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The fragmented and labeled sscDNA (5.5 µg) was then hybridized to Affymetrix Mouse Transcriptome 1.0 arrays (MTA 1.0) at 48ºC for 17h and subsequently washed and stained using Affymetrix proprietary reagents in the GeneChip Fluidics Station 450 (FS450).
|
| Scan protocol |
GeneChips were scanned in the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
WT BMDC Unloaded-1
Gene expression data
|
| Data processing |
CEL files generated after MTA 1.0 GeneChip scanning were uploaded onto the Expression Console software for analysis with SST-RMA algorithm (Affymetrix).
|
| |
|
| Submission date |
Aug 04, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Dan Liang |
| Organization name |
Baylor college of medicine
|
| Department |
Pathology and Immunology
|
| Street address |
One baylor plaza, Room N920
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030-3498 |
| Country |
USA |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE102282 |
Expression data from WT and AIMp1KO mouse bone marrow-derived dendritic cells |
|
