|
| Status |
Public on Apr 09, 2019 |
| Title |
IRF5_3 |
| Sample type |
RNA |
| |
|
| Source name |
F4/80+, CD11b+ peritoneal macrophage isolated from ovarian tumor mouse received 2 i.p. doses of nanoparticles carrying 30 microgram mIRF5 mRNA treatment.
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Nanoparticles carrying mIRF5 mRNA
cell type: F4/80+, CD11b+ peritoneal macrophage
strain: C57BL/6J
|
| Treatment protocol |
After 7 weeks of tumor innoculation, mice received 2 doses of i.p. injection (day 1 and day 5) of either (1) PBS, or (2) nanoparticles carrying 30 microgram of mIRF5 mRNA.
|
| Growth protocol |
ID8 cells were injected to adult C57BL/6J mice 7 weeks before treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peritoneal cells were first isolated through peritoneal lavage, followed with FACS isolation of F4/80+, CD11b+ peritoneal macrophage
|
| Label |
na
|
| Label protocol |
Ligation master mix (provided by NanoString) was added to the mRNA solution and incubated under 48 °C for 5min to allow ligation, followed with purification to remove unligated molecules.
|
| |
|
| Hybridization protocol |
The ligated RNA were co-incubated with miRNA capture probeset, miRNA reporter codeset in hybridization buffer following the protocol provided by NanoString. The hybridation happened in 65 °C for at least 12 hours.
|
| Scan protocol |
All samples were read on nCounter Analysis System (NanoString Technologies).
|
| Description |
IRF5_3
|
| Data processing |
Raw data was processed and checked for quality using the R/Bioconductor package NanoStringQCPro (Nickles D, Sandmann T, Ziman R and Bourgon R (2017). NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data. R package version 1.10.0.). Expression values were normalized to the geometric mean of housekeeping genes and log2-transformed using nSolver 4.0 software (NanoString Technologies). FDR for ratio data was calculated from the p-values returned by the t-test using the Benjamini-Yekutieli method.
|
| |
|
| Submission date |
Apr 08, 2019 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Matthias Stephan |
| Organization name |
Fred Hutchinson Cancer Research Institute
|
| Street address |
1100 Fairview Ave. N., Thomas Research Buildin
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-9024 |
| Country |
USA |
| |
|
| Platform ID |
GPL25266 |
| Series (1) |
| GSE129498 |
Identify signature genes associated with nanoparticle carrying IRF5 mRNA treatment in isolated peritoneal macrophages from ID8 cells-induced ovarian tumor mouse |
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