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Sample GSM579137 Query DataSets for GSM579137
Status Public on Jan 01, 2011
Title Macrophage Kdo2 1h Expression (Cy5)
Sample type RNA
 
Source name thioglycollate-elicited peritoneal macrophages
Organism Mus musculus
Characteristics cell type: thioglycollate-elicited peritoneal macrophages
treatment: Kdo2 for 1 hour
strain: C57BL/6
Growth protocol CD43-negative splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells using MACS (Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS. Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer.
Label Cy5
Label protocol Total RNA (250 ng) of two biological replicates was amplified and labeled using the Agilent Quick-Amp labeling kit according to the manufacturer's instructions.
 
Hybridization protocol 4x 44 k Agilent arrays were hybridized with 825 ng of each cDNA using the manufacturer's hybridization kit according to the instructions.
Scan protocol Scanned on an Agilent Technologies Scanner using the extended dynamic range scan mode with a 5 µm pitch.
Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).
Description Macrophage Expression in response to Kdo2 at 1 hour
Raw data file: US22502657_251486819799_S01_GE2-v5_95_Feb07_1_2.txt
Data processing Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Data was further normalized between arrays using a multi-loess technique described in Corbeil et al (Journal of Molecular Endocrinology (2004) 33:1–9).
Dual-channel hybridization was analyzed as single-channel (ratios were not used). Each channel of biological replicates is therefore represented as a single Sample and the same raw data file is linked to two Sample records.
 
Submission date Aug 13, 2010
Last update date Jan 01, 2011
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platform ID GPL7202
Series (2)
GSE23620 Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (Agilent expression data)
GSE23622 Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

Data table header descriptions
ID_REF
VALUE Normalized probe intensity for each channel

Data table
ID_REF VALUE
A_52_P616356 89.4
A_52_P403405 46.1
A_52_P819156 43.5
A_51_P331831 4326.6
A_51_P430630 43.7
A_52_P502357 39.2
A_52_P299964 47.6
A_51_P356389 46.5
A_52_P684402 210.7
A_51_P414208 50.6
A_51_P280918 216.3
A_52_P613688 479.7
A_52_P258194 53.8
A_52_P229271 61.2
A_52_P579519 275.5
A_52_P979997 39.6
A_52_P453864 39.7
A_52_P655842 52.7
A_51_P282374 40.1
A_52_P176013 81.2

Total number of rows: 38516

Table truncated, full table size 692 Kbytes.




Supplementary file Size Download File type/resource
GSM579137_US22502657_251486819799_S01_GE2-v5_95_Feb07_1_2_ch1.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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