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Sample GSM357494 Query DataSets for GSM357494
Status Public on Feb 05, 2009
Title 251486814895_A03
Sample type RNA
 
Channel 1
Source name J774A.1_EBSS+SB202190_6hours
Organism Mus musculus
Characteristics J774A.1 cells incubated in Earle’s Balanced Salt Solution (EBSS) for 6 hours in the presence of the p38 inhibitor SB202190 (10 µM)
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from cultured cells using the Absolutely RNA Miniprep Kit (Stratagene, La Jolla, CA). All RNA samples were treated with RNase-free DNase I. RNA quality was verified on an Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).
Label Cy5
Label protocol Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy5 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy5 incorporation at 650 nm using a Nanodrop.
 
Channel 2
Source name J774A.1_RPMI_6hours
Organism Mus musculus
Characteristics J774A.1 cells incubated in RPMI 1640 medium supplemented with 10% fetal bovine serum for 6 hours
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from cultured cells using the Absolutely RNA Miniprep Kit (Stratagene, La Jolla, CA). All RNA samples were treated with RNase-free DNase I. RNA quality was verified on an Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).
Label Cy3
Label protocol Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy5 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy3 incorporation at 550 nm using a Nanodrop.
 
 
Hybridization protocol For Cy3 14pmol and for Cy5 10 pmol incorporated dye was fragmented and resuspended in 55 ul hybridization solution (Agilent). The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.
Scan protocol After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' and images were processed with the Feature Extraction Software version 9.5 (Agilent).
Description Phagocytosis represents a mechanism used by macrophages to remove pathogens and cellular debris. Recent evidence suggested that amino acid or glucose deprivation may cause an increase in phagocytosis of heat-inactivated Escherichia coli and Staphylococcus aureus by macrophages, but not the uptake of platelets, apoptotic cells or beads. Increased phagocytosis of bacteria could be blocked by phagocytosis inhibitors and depended on p38 MAP kinase activity. To examine potentially important downstream pathways linked to EBSS-induced starvation and p38 MAP kinase activation, a full genome microarray representing over 41,000 mouse genes or transcripts was probed with cDNA isolated from J774A.1 macrophages that were treated with EBSS, EBSS supplemented with the p38 inhibitor SB202190 or control medium supplemented with 10% fetal bovine serum.
Data processing Log-ratio of the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. In case of multiple probes for the same Agilent ID, log-ratios were averaged.
 
Submission date Jan 06, 2009
Last update date Mar 02, 2009
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL7202
Series (1)
GSE14293 Transcriptome analysis of J774A.1 macrophages undergoing amino acid deprivation

Data table header descriptions
ID_REF
VALUE log ratios of Cy5/Cy3

Data table
ID_REF VALUE
A_51_P100021 -0.196149106
A_51_P100034 0.192239237
A_51_P100052 -0.177174158
A_51_P100063 1.009322111
A_51_P100084 1.276671496
A_51_P100099 -0.047087698
A_51_P100155 0.326552777
A_51_P100174 -1.858667202
A_51_P100181 -0.426331381
A_51_P100218 -0.150716185
A_51_P100227 -0.040509892
A_51_P100238 -1.124161822
A_51_P100246 -0.198174393
A_51_P100289 -0.02304208
A_51_P100298 1.330553801
A_51_P100309 -0.217176605
A_51_P100327 0.413958559
A_51_P100347 -0.254758786
A_51_P100379 0.322844639
A_51_P100428 -0.271412383

Total number of rows: 41174

Table truncated, full table size 1024 Kbytes.




Supplementary file Size Download File type/resource
GSM357494.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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