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Sample GSM478121 Query DataSets for GSM478121
Status Public on Mar 01, 2010
Title 3_14_TNFa_4h_rep3
Sample type RNA
Source name primary murine hepatocytes cultivated on collagen coated plates
Organism Mus musculus
Characteristics tissue: liver
gender: male
agent: TNFa
time: 4h
Extracted molecule total RNA
Extraction protocol RNA was prepared from cultured hepatocytes with the Qiagen RNEasy plus Kit according to the manufactures instructions. For each sample, 2 million cells were used for RNA isolation and purification. Samples for microarray analysis were subjected to a quality control using an Agilent Bioanalyzer with the Pico RNA-Kit. Only RNA with a RIN better than 8.2 was used for labeling and subsequent hybridization.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
Scan protocol Affymetrix GeneArray Scanner3001
Description Gene expression data from primary mouse hepatocytes
Data processing Mouse430V2 Affymetrix CEL data files were uploaded into Expressionist Refiner Array® version 4.5 (Genedata AG, Basel, Switzerland) for data condensation. Oligo hybridization intensities were condensed to probe set expression values using the MAS5 Affymetrix Statistical algorithm according to [60]. Condensed data were normalized using Expressionist Analyst® version 4.5 (Genedata AG, Basel, Switzerland). The mapping from probe-sets to genes was performed using the Phylosopher seqmap tool based on the NCBI mouse genome version 33. Absolute probe set expression values were scaled on the chip level by logarithmic mean normalization (for each chip, the geometric mean of all probe set values was scaled to 10000).
Submission date Dec 02, 2009
Last update date Jan 22, 2010
Contact name Irmgard Merfort
Organization name University of Freiburg - Institute of Pharmaceutical Science
Department Department of Pharmaceutical Biology and Biotechnology
Lab Merfort
Street address Stefan-Meier-Str. 19
City Freiburg
State/province BW
ZIP/Postal code 79104
Country Germany
Platform ID GPL1261
Series (1)
GSE19272 Genome-wide comparison between IL-17 and combined TNF-alpha/ IL-17 induced genes in primary murine hepatocytes

Data table header descriptions
VALUE MAS5.0 signal intensity

Data table
AFFX-BioB-5_at 94591
AFFX-BioB-M_at 138788
AFFX-BioC-5_at 257193
AFFX-BioDn-5_at 542051
AFFX-CreX-5_at 2624956
AFFX-CreX-3_at 3145544
AFFX-ThrX-5_at 57152
AFFX-b-ActinMur/M12481_5_at 3846547
AFFX-b-ActinMur/M12481_M_at 3751813
AFFX-b-ActinMur/M12481_3_at 4669180
AFFX-GapdhMur/M32599_5_at 4523030
AFFX-GapdhMur/M32599_M_at 4109133
AFFX-GapdhMur/M32599_3_at 3485304
AFFX-TransRecMur/X57349_5_at 77914
AFFX-TransRecMur/X57349_M_at 52481
AFFX-TransRecMur/X57349_3_at 142222
AFFX-PyruCarbMur/L09192_5_at 50923
AFFX-PyruCarbMur/L09192_MA_at 68838
AFFX-PyruCarbMur/L09192_MB_at 69674
AFFX-PyruCarbMur/L09192_3_at 126860

Total number of rows: 45101

Table truncated, full table size 744 Kbytes.

Supplementary file Size Download File type/resource
GSM478121.CEL.gz 6.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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