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Series GSE11449 Query DataSets for GSE11449
Status Public on Jun 28, 2008
Title RAW264.7 cells were treated with KDO, IFN beta and 8Br
Organism Mus musculus
Experiment type Expression profiling by array
Summary RAW 264.7 cells were stimulated with KDO (100 ng/ml), IFN-β (300 pM) and/or 8-Br 100 μM. These ligands were applied individually or in combination with KDO for 60 min and 120 min. Total RNA was extracted using TriPure (Roche) following its protocol.
Keywords: designed
 
Overall design
RAW 264.7 cells were stimulated with KDO (100 ng/ml), IFN-β (300 pM) and/or 8-Br 100 μM. These ligands were applied individually or in combination with KDO for 60 min and 120 min. Total RNA was extracted using TriPure (Roche) following its protocol. The detailed procedure is available at http://www.signaling-gateway.org/data/ProtocolLinks.html (AfCS Procedure Protocol PP00000009). Duplicate experiments were done for each treatment.

Oligonucleotide array fabrication and annotation
16 K mouse oligonucleotide arrays were fabricated with 15,631 oligomers of 65-bp or 70-bp long. The oligomers were purchased from Operon and Sigma-Genosys and were inkjet-printed onto glass slides by Agilent Technologies. The list of genes is available through the GEO (Gene Expression Omnibus - http://www.ncbi.nlm.nih.gov/geo) as an accession number GPL254.

Gene expression analysis
The hybridization experiment and analysis were performed as previously described (Park et al., 2004; Zhu et al., 2006; Zhu et al., 2004). Cy5-labeled cRNA (RNA of ligand treated cells) and Cy3-labeled cRNA (RNA of time matched controls) were hybridized in the array. Dye-swap labeling was performed for each pair of samples. The arrays were scanned with Agilent Scanner G2505A (Agilent Technologies) and image files were extracted with background subtraction and dye-normalization using Agilent G2566AA Extraction Software version A.6.1.1 (Agilent Technologies).
 
Contributor(s) Hart R, Chang M, Hsueh R, Choi S, Kim J, Cao Y, Lee S, Alexander A, Grossoehme J, Yan Z
Citation(s) 23166526
Submission date May 15, 2008
Last update date Jan 08, 2013
Contact name Sangdun Choi
E-mail(s) [email protected]
Phone 626-395-8732
URL http://www.signaling-gateway.org
Organization name California Institute of Technology
Department Biology
Lab Alliance for Cellular Signaling Molecular Biology Laboratory
Street address 1200 E. California Blvd
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
 
Platforms (1)
GPL254 Caltech 16K Oligo Mouse Array
Samples (28)
GSM288409 16000508000625_UT 60min_1 vs UT 60min_2_A01 Untreated RAW264.7 cells
GSM288410 16000508000625_UT 60min_2 vs UT 60min_1_A02
GSM288411 16000508000636_KDO (EYC060227A06) 60min vs UT 60min RAW 264.7 cells
Relations
BioProject PRJNA106481

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11449_RAW.tar 83.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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