|
| Status |
Public on Mar 19, 2019 |
| Title |
M2 BMDM of Dner-deficient mice_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Dner deficient
strain: C57BL/6N
|
| Treatment protocol |
As described in the paper. Briefly, bone marrow was flushed from femurs and tibias of C57BL/6N and Dner-/- mice with RPMI-1640 medium. Bone marrow cells were passed through 40µm filters (Miltenyi Biotec), counted and resuspended in 5% fetal bovine serum, 50μM β-mercaptoethanol and 100 U/ml penicillin and streptomycin RPMI-1640 medium. 2x10^6 cells/mL were plated in 24 well plates for RNA isolation. Medium was additionally supplemented with 20ng/mL of murine recombinant M-CSF to generate bone marrow derived macrophages (BMDM). Cells were maintained at 37°C, 5% CO2 for 7 days changing medium every 2-3 days and carefully discarding non-adherent cells. For BMDM, on day 7 fresh medium without M-CSF was added and left overnight. BMDM were stimulated with 1µg/mL LPS (from E.coli 0111:B4, Sigma-Aldrich) and 20ng/mL of recombinant murine IFNγ (M1 phenotype) or with 20ng/mL of recombinant murine IL-4 (M2 phenotype) for 24h.
|
| Growth protocol |
no
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with peqGOLD total RNA kit (Peqlab) including digestion of remaining genomic DNA
|
| Label |
biotin
|
| Label protocol |
Ovation Pico WTA System V2 in combination with the Encore Biotin Module (NuGEN Technologies, Inc, San Carlos, CA, USA)
|
| |
|
| Hybridization protocol |
According to the Affymetrix expression protocol (HWS kit) including minor modifications according to the Nugen protocol
|
| Scan protocol |
According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)
|
| Description |
Gene expression data from M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 1
|
| Data processing |
Expression console (v.1.4.1.46, Affymetrix) was used for quality control and to obtain annotated normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation)
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| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Johannes Beckers |
| E-mail(s) |
johannes.beckers@helmholtz-munich.de
|
| Organization name |
Helmholtz Zentrum Muenchen
|
| Department |
Institute of Experimental Genetics
|
| Street address |
Ingolstaedter Landstr. 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE119257 |
The non-canonical Notch ligand DNER regulates IFNγ in macrophages during COPD progression |
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