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Sample GSM379302 Query DataSets for GSM379302
Status Public on Jan 10, 2010
Title wt_3hTNF_rep1
Sample type RNA
Source name p65 wt MEFs, 3h TNF, replicate 1
Organism Mus musculus
Characteristics cell line: Mouse embryonic fibroblasts
Treatment protocol Cells were starved overnight before either left untreated or stimulated with 30 ng/ml mouse TNFα for 3 hours.
Growth protocol Cells were maintained in DMEM supplemented with 10% FCS, 100 units/ml penicillin/streptomycin and non-essential amino acids.
Extracted molecule total RNA
Extraction protocol Total RNA from three biological replicates per sample was isolated at different days using the ‘Total RNA isolation mini kit’ (Agilent Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol RNA was labeled using the ‘Agilent Low RNA Input Linear Amplification Kit PLUS’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the ND-1000 Spectrophotometer (NanoDrop Technologies).
Hybridization protocol 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the DNA Microarray-Scanner with Surescan High-Resolution Technology (Agilent Technologies) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, eCtended Dynamic range selected, Dye channel is set to Green, Green PMT XDR Hi is set to 100% and Green PMT XDR Lo to 10%).
Description Gene expression after 3 hours of TNFalpha stimulation from p65(-/-) MEFs genetically complemented with p65 wild type
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_v5_91_0806 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data was normalized with default settings using ‘Rosetta Resolver® Gene Expression Data Management and Analysis System’ (Rosetta Biosoftware).
Submission date Mar 11, 2009
Last update date Jan 02, 2010
Contact name Karin Rothgiesser
Organization name Institute of Veterinary Biochemistry and Molecular Biology
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
Platform ID GPL7202
Series (1)
GSE15196 Acetylation of p65 at lysine 314 is important for late NF-k(kappa)B-dependent gene expression

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_52_P136751 289.84158
A_52_P1156465 452.052
A_52_P661982 11293.578
A_52_P779137 9.2530365
A_51_P428086 441.6418
A_52_P271894 67.30635
A_51_P403693 11989.677
(+)E1A_r60_a20 581.85455
A_52_P812372 9.55086
A_51_P148587 9.30528
A_52_P272936 22.803852
A_51_P405496 21.124498
A_51_P345110 7304.2407
A_51_P244234 9.505105
A_52_P205710 14.555836
A_51_P410892 6769.0605
A_51_P258698 4930.5703
A_52_P107923 13.326889
A_52_P395685 8.787566
A_51_P127738 71.02645

Total number of rows: 41266

Table truncated, full table size 906 Kbytes.

Supplementary file Size Download File type/resource
GSM379302.txt.gz 5.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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