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Sample GSM1018157 Query DataSets for GSM1018157
Status Public on Apr 11, 2013
Title TRIF 3 (4h) - vs. TRIF 3 (4h) LPS
Sample type RNA
 
Channel 1
Source name TRIF 3 (4h) untreated
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: BMDM (bone marrow derived macrophages)
treatment: naive
genotype/variation: TRIF -/- KO
time: 4h
Treatment protocol Cells were stimulated with 200 ng/mL LPS (Salmonella minessota, ultrapure, Invivogen) in serum-free DMEM without phenolred or left untreated. At 1, 2, 4, 8 or 16 hours, cell supernatants were collected, passed through a 0.22 µm filter to remove detached cells, aliquotted and immediately frozen in liquid nitrogen.
Growth protocol Bone marrow was collected from femur and tibia of age and gender matched mice of the indicated genotypes. Bone marrow cells were plated on sterile petridishes and incubated in DMEM containing 10% FCS, 5% equine serum, 10 mM HEPES, 1 mM pyruvate, 10 mM L-glutamine, and 20% M-CSF–conditioned medium at 37 °C and 7% CO2. M-CSF–conditioned medium was collected from an L929 M-CSF cell line. Bone marrow derived macrophages were harvested after 6 days and replated in tissue-culture treated dishes. Before the experiment, cells were washed once with serum-free DMEM without phenolred.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.
Label Cy3
Label protocol Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies).
 
Channel 2
Source name TRIF 3 (4h) LPS-treated
Organism Mus musculus
Characteristics strain: C57BL/6
cells: BMDM (bone marrow derived macrophages)
treatment: LPS
genotype/variation: TRIF -/- KO
time: 4h
Treatment protocol Cells were stimulated with 200 ng/mL LPS (Salmonella minessota, ultrapure, Invivogen) in serum-free DMEM without phenolred or left untreated. At 1, 2, 4, 8 or 16 hours, cell supernatants were collected, passed through a 0.22 µm filter to remove detached cells, aliquotted and immediately frozen in liquid nitrogen.
Growth protocol Bone marrow was collected from femur and tibia of age and gender matched mice of the indicated genotypes. Bone marrow cells were plated on sterile petridishes and incubated in DMEM containing 10% FCS, 5% equine serum, 10 mM HEPES, 1 mM pyruvate, 10 mM L-glutamine, and 20% M-CSF–conditioned medium at 37 °C and 7% CO2. M-CSF–conditioned medium was collected from an L929 M-CSF cell line. Bone marrow derived macrophages were harvested after 6 days and replated in tissue-culture treated dishes. Before the experiment, cells were washed once with serum-free DMEM without phenolred.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.
Label Cy5
Label protocol Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies).
 
 
Hybridization protocol After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies).
Scan protocol Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).
Description untreated vs LPS treated
Data processing Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies).
The normalized/processed data are included in the LogRatio column of the Agilent Feature Extraction files (ie, normalized log10 Cy5/Cy3 ratios).
Note: The NA probes of Platform GPL10333 are not present in the Agilent FE files.
 
Submission date Oct 11, 2012
Last update date Apr 12, 2013
Contact name Hans-Joachim Mollenkopf
E-mail(s) mollenkopf@mpiib-berlin.mpg.de
Phone +49 30 28460 482
Organization name Max-Planck-Institute for Infection Biology
Lab Microarray/Genomics Core Facility
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL10333
Series (1)
GSE41490 Direct proteomic quantification of the secretome of activated immune cells

Data table header descriptions
ID_REF
VALUE normalized log10 Cy5/Cy3 ratio

Data table
ID_REF VALUE
1 -0.08847634
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 -0.07385942
13 0.256124456
14 -0.101694727
15 0.075843266
16 -0.304618249
17 0.098421455
18 0
19 0.012719567
20 0

Total number of rows: 45220

Table truncated, full table size 699 Kbytes.




Supplementary file Size Download File type/resource
GSM1018157_US22502595_252665513722_S01_GE2_1010_Sep10_1_4.txt.gz 15.4 Mb (ftp)(http) TXT
GSM1018157_US22502595_252665513722_S01_GE2_1010_Sep10_1_4_MAGEML.xml.gz 8.0 Mb (ftp)(http) XML
Processed data included within Sample table
Processed data provided as supplementary file

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