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Sample GSM3362372 Query DataSets for GSM3362372
Status Public on Mar 19, 2019
Title M2 BMDM of Dner-deficient mice_rep3
Sample type RNA
 
Source name M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 3
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 3
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)
 
Submission date Aug 30, 2018
Last update date Mar 22, 2019
Contact name Johannes Beckers
E-mail(s) beckers@helmholtz-muenchen.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

Data table header descriptions
ID_REF
VALUE RMA signal intensity (log2)

Data table
ID_REF VALUE
17210850 2.658
17210852 2.764
17210855 8.936
17210869 10.168
17210883 3.311
17210887 8.611
17210904 3.773
17210912 8.060
17210947 3.033
17210953 5.218
17210984 9.024
17210994 3.381
17210996 3.540
17210998 2.966
17211000 6.531
17211004 5.183
17211023 4.821
17211033 3.292
17211043 8.728
17211066 2.757

Total number of rows: 41345

Table truncated, full table size 607 Kbytes.




Supplementary file Size Download File type/resource
GSM3362372_Dner_M2_3.CEL.gz 8.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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