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Sample GSM485848 Query DataSets for GSM485848
Status Public on Mar 29, 2012
Title TEPM-0h LPS-rep3
Sample type RNA
 
Source name Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h
Organism Mus musculus
Characteristics strain: C57Bl/6
gender: male
tissue: peritoneal
cell type: macrophages
treatment: untreated
treatment time: 0 hours
Treatment protocol BMM and TEPM were treated for various times with lipopolysaccharide (LPS) from Salmonella minnesota (Sigma-Aldrich), at a final concentration of 10 ng/ml.
Growth protocol BMM were derived from femurs of 6-8 week-old, male C57Bl/6 mice. Femurs were flushed with medium and bone marrow cells were plated out in complete medium (RPMI 1640 containing 10% FCS, 20U/ml penicillin, 20 µg/ml streptomycin and 2mM L-glutamine) supplemented with 104U/ml (100ng/ml) recombinant human CSF-1 (Chiron) on bacteriological plastic plates (Bibby Sterilin) for 7 days, with refeeding on day 5 and reseeding on day 6 at 1x105 cells/cm2. TEPM were elicited by injecting 6-8 week-old male, mice with 1ml sterile thioglycollate broth (10% in pyrogen-free water, Becton Dickinson) intraperitoneally. 5 days post-injection, peritoneal cells were collected by PBS lavage, plated on tissue culture plastic as for BMM in media without CSF-1 and stimulated the following day. >90% TEPM were F4/80+ macrophages, as assessed by surface staining and flow cytometry (not shown). All cells were cultured at 37˚C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using the Qiagen RNeasy Mini kit with on-column DNaseI treatment, according to the manufacturer’s instructions.
Label Cy3
Label protocol Labelling was performed using the Agilent Quick-Amp Labelling Kit (one colour) according to manufacturer's instructions.
 
Hybridization protocol Samples were hybridised according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008.
Scan protocol Samples were scanned according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008, using an Agilent Microarray Scanner G2565BA.
Description TEPM-0h LPS-rep3
Data processing Features (including processed signal and flags) were extracted using the Feature Extraction 9.5.3 (Agilent Technologies) software, with default settings and no background subtraction. Processed signal intensities were quantile normalized in R using the Affymetrix package in Bioconductor.
 
Submission date Dec 15, 2009
Last update date Mar 29, 2012
Contact name Kate Schroder
E-mail(s) K.Schroder@imb.uq.edu.au
Phone +617 33462087
Fax +617 33462101
Organization name Institute for Molecular Bioscience
Street address University of Queensland, St Lucia
City Brisbane
State/province QLD
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL9802
Series (2)
GSE19490 Transcriptional responses of mouse BMM and TEPM to lipopolysaccharide (LPS)
GSE19492 Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ENSMUSG00000000056-1 0.46658295
ENSMUSG00000000056-2 0.5795158
ENSMUSG00000000056-3 0.61181575
ENSMUSG00000000056-4 0.85353816
ENSMUSG00000000148-1 1.1313646
ENSMUSG00000000148-2 1.000729
ENSMUSG00000000148-3 1.1716576
ENSMUSG00000000148-4 1.2141335
ENSMUSG00000000148-5 0.7607419
ENSMUSG00000000148-6 1.1980864
ENSMUSG00000000148-7 0.6366984
ENSMUSG00000000148-8 1.0314434
ENSMUSG00000000149-1 1.4899011
ENSMUSG00000000149-2 1.514797
ENSMUSG00000000149-3 1.3984878
ENSMUSG00000000149-4 1.3337909
ENSMUSG00000000184-1 0.16273618
ENSMUSG00000000184-2 0.117685884
ENSMUSG00000000184-3 0.07490536
ENSMUSG00000000184-4 0.08788357

Total number of rows: 15208

Table truncated, full table size 472 Kbytes.




Supplementary file Size Download File type/resource
GSM485848.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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