|
| Status |
Public on Mar 08, 2017 |
| Title |
tumor-untreated-rep4 |
| Sample type |
RNA |
| |
|
| Source name |
EG7-OVA tumor subcutanous, 9 days after treatment
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
tissue: tumor EG7-OVA cells
sample collection time: 9 days post treatment
|
| Treatment protocol |
EG7-OVA tumor cells were implanted subcutaneously into the flank of C57BL/6 mice. When tumors became palpable (d7), they were treated with artLCMV-OVA or left untreated. Tumor tissue was analyzed on d9 after treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissue was collected in 1ml QIAzol (QIAGEN) and homogenized using a metal bead and the QIAGEN Tissue Lyser. RNA was extracted with a standard isopropanol precipitation method according to the manufacturer's instructions.
|
| Label |
none
|
| Label protocol |
not applicable
|
| |
|
| Hybridization protocol |
100 ng of total RNA were hybridized overnight at 65°C with the nanostring Mm v2 Inflammation codeset according to manufacturer specification. Target-probe complexes were purified on the nCounter Prep Station
|
| Scan protocol |
Cartridges were scaned on the Gen1 nCounter Digital Analyzer asking for 1155 FOV
|
| Description |
untreated
|
| Data processing |
Raw counts as provided by the nCounter assay were scale-normalized using the TMM method implemented in the calcNormFactors function of the R package edgeR (McCarthy et al. 2012). The transformed counts (log-CPM values) were subsequently used for linear modelling.
|
| |
|
| Submission date |
Jul 05, 2016 |
| Last update date |
Nov 18, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
|
| Organization name |
University of Basel
|
| Department |
Departement of Biomedicine
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL20885 |
| Series (1) |
| GSE84039 |
Development of live-attenuated lymphocytic choriomeningitis virus vectors for potent alarmin-driven CD8+ T cell induction in tumor immunotherapy |
|
