|
| Status |
Public on Sep 19, 2016 |
| Title |
Spleen_anti-Gr1_3 |
| Sample type |
RNA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
tissue: spleen
gender: male
age: 8 weeks old
|
| Treatment protocol |
αIFNAR and isotype control antibody were administred i.p. one day prior to infection at a dose of 1mg per mouse. αGR-1 antibody was administered 2 days and half a day prior to infection at a dose of 500ug ip
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested directly in Trizol, after homogeneization of the tissue, phase separation was performed with chloroform and RNA was precipitated with Isopropanol and washed with ethanol according to standard procedures.
|
| Label |
none
|
| Label protocol |
none
|
| |
|
| 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 |
tissue: Spleen, treatment: anti-Gr1, annimal id: 3, batch: 20160107
|
| Data processing |
The read.markup.RCC function the R package NanoStringNorm (Waggott, D.M., 2015) was used to read the raw count data. Raw counts 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 (2) |
| GSE84036 |
Type-I-Interferons induce the decimation of antiviral B cells at the onset of chronic infection [nanostring] |
| GSE84038 |
Type-I-Interferons induce the decimation of antiviral B cells at the onset of chronic infection |
|
