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Sample GSM691431 Query DataSets for GSM691431
Status Public on May 22, 2011
Title macrophage_TrifKO_control_rep1
Sample type RNA
 
Source name bone marrow derived macrophages from Trif knockout mice, not stimulated
Organism Mus musculus
Characteristics strain: C57BL6/J
gender: Female
age: 5-6 weeks
genotype/variation: Trf1 knock out
cell type: bone marrow macrophage (BMM)
protocol: control
time: 0h
Treatment protocol The cultured bone marrow derived macrophages (BMMs) were detached and re-plated 4 hours prior to the experiment. At the start of the experiment, BMMs were incubated with viable E. coli for the 1, 3 or 6 hours. Bacteria were used at a multiplicity of infection (MOI) of 20. All experiments were carried out in antibiotic free 'complete medium'. One hour after addition of viable bacteria, penicillin (100μg/ml) and streptomycin (100μg/ml) were added to the media in order to kill any remaining extracellular bacteria. For transcriptional analysis three independent experiments were performed. We compared this approach to washing the cells and replacing the antibiotic free medium with penicillin/streptomycin containing medium after one hour and found no differences with regards to the cellular responses measured.
Growth protocol Murine macrophages, derived from the bone marrow of either C57BL/6J, or Trif-/- mice, were cultured in RPMI 1640 supplemented with macrophage colony-stimulating factor (M-CSF) and 10% FBS, plus 100μg/ml penicillin, 100μg/ml streptomycin, 10mM HEPES and 1nM sodium pyruvate (all obtained from Sigma-Aldrich).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the BMMs using the RNeasy kit (QIAGEN). RNA from RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.
Label biotin
Label protocol The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).
 
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Description KO_ctr0h_1
G004_E05_05_113-5_KO_ctr0h.CEL
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.14.0).
 
Submission date Mar 15, 2011
Last update date May 22, 2011
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11533
Series (1)
GSE27960 Sensing prokaryotic mRNA signifies microbial viability and promotes immunity

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

Data table
ID_REF VALUE
10338001 11.27472159
10338002 4.936767469
10338003 9.332866053
10338004 8.420353746
10338005 2.429937017
10338006 2.643271286
10338007 2.919878678
10338008 3.217812411
10338009 7.041203206
10338010 2.467657577
10338011 4.324232812
10338012 2.54749885
10338013 2.272412021
10338014 2.353221064
10338015 2.290351407
10338016 5.896602748
10338017 12.49832306
10338018 5.383550319
10338019 3.95134208
10338020 6.701275955

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM691431.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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