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Sample GSM880665 Query DataSets for GSM880665
Status Public on Sep 19, 2012
Title Sham_FSAP-/-.3
Sample type RNA
 
Source name liver
Organism Mus musculus
Characteristics background strain: BalbC
group: sham-operated
genotype/variation: FSAP-deficient
Treatment protocol FSAP-/- mice were backcrossed on to the BalbC background up to the F3 generation. FSAP-/- and littermate FSAP+/+ (WT) mice obtained from crossings between heterozygous mice were used for the experiment between 20 and 30 weeks of age. Surgical ligation of the common bile duct (BDL) was performed under isoflurane anesthesia and sham-operated mice underwent the same procedures except that the bile duct was not ligated. After 2 weeks the mice were sacrificed and the liver was flash frozen and stored at -80°C for further analysis.
Extracted molecule total RNA
Extraction protocol Liver RNA was isolated by guanidine thiocyanate, chloroform and isopropanol precipitation, followed by DNAase digestion. Quantification and quality control of the RNA was checked with Agilent 2100 Bioanalyzer platform (Agilent Technologies, Palo Alto, CA, USA). Only total RNA with an RNA integrity number ≥ 7.2 was used for microarray hybridization (N = 3 mice per group)
Label Cy3
Label protocol 100 ng of each total RNA samples was used for the amplification and labeling step using the Agilent Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
 
Hybridization protocol The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.7, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software 9.1 was used to read out and process the microarray image files.
Data processing FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).
 
Submission date Feb 24, 2012
Last update date Sep 19, 2012
Contact name Ute Bissels
E-mail(s) ute.bissels@miltenyibiotec.de
Organization name Miltenyi Biotec GmbH
Department R&D
Street address Friedrich-Ebert-Str. 68
City Bergisch Gladbach
State/province NRW
ZIP/Postal code 51429
Country Germany
 
Platform ID GPL11202
Series (1)
GSE36066 Factor VII activating protease (FSAP) exerts antifibrotic effects in a mouse model of experimental liver fibrosis

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity data (w/o controls) in log2 space.

Data table
ID_REF VALUE
A_52_P275259 2.214
A_55_P1983944 3.871
A_52_P585448 11.679
A_55_P2097560 7.300
A_51_P421876 8.252
A_51_P400016 11.173
A_55_P2162497 2.276
A_52_P27122 5.647
A_55_P2015173 2.159
A_55_P2009217 11.874
A_55_P2078955 11.062
A_55_P2139814 5.416
A_55_P2225178 2.728
A_51_P317640 2.096
A_55_P1970234 5.858
A_55_P2005225 6.183
A_55_P1970831 2.487
A_51_P253857 2.276
A_55_P2017724 8.614
A_55_P2030020 2.389

Total number of rows: 39429

Table truncated, full table size 763 Kbytes.




Supplementary file Size Download File type/resource
GSM880665_252665511317_1_1.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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