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Sample GSM3362367 Query DataSets for GSM3362367
Status Public on Mar 19, 2019
Title M1 BMDM of Dner-deficient mice_rep1
Sample type RNA
 
Source name M1 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 M1 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)
 
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 2.568
17210852 2.948
17210855 9.036
17210869 10.139
17210883 3.086
17210887 8.322
17210904 4.026
17210912 8.343
17210947 3.029
17210953 6.271
17210984 9.028
17210994 3.127
17210996 3.286
17210998 2.685
17211000 5.770
17211004 4.617
17211023 3.932
17211033 3.781
17211043 8.011
17211066 2.897

Total number of rows: 41345

Table truncated, full table size 607 Kbytes.




Supplementary file Size Download File type/resource
GSM3362367_Dner_M1_1.CEL.gz 8.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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