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Sample GSM3362371 Query DataSets for GSM3362371
Status Public on Mar 19, 2019
Title M2 BMDM of Dner-deficient mice_rep2
Sample type RNA
 
Source name M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 2
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 2
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 2.803
17210852 2.764
17210855 9.183
17210869 10.142
17210883 3.028
17210887 8.468
17210904 3.450
17210912 7.990
17210947 3.054
17210953 5.184
17210984 8.950
17210994 3.338
17210996 3.436
17210998 2.944
17211000 6.998
17211004 5.159
17211023 4.077
17211033 3.313
17211043 9.010
17211066 2.997

Total number of rows: 41345

Table truncated, full table size 607 Kbytes.




Supplementary file Size Download File type/resource
GSM3362371_Dner_M2_2.CEL.gz 8.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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