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Sample GSM864797 Query DataSets for GSM864797
Status Public on Mar 31, 2013
Title WT ligament tissue
Sample type RNA
 
Source name ligament tissue from wild type mice
Organism Mus musculus
Characteristics background strain: C57BL/6J
genotype: wild type
tissue: ligament
Growth protocol Mesenchymal stem cells (sample 1) derived from mouse embryos were obtained from the Cell Bank RIKEN Bioresource Center, Japan. The cells were suspended in E-MEM and Dulbecco’s Modified Eagle’s medium containing 10% foetal bovine serum (FBS) to a final concentration of 1.5 × 10^5 cells/ml, were seeded into dishes or flasks (2.0 × 10^4 cells/cm2), and were statically cultured at 37°C under 5% CO2. For the expression of murine proteins, the synthesized mouse A sequence was inserted into XhoI of the pCAGGS vector, which was then cloned and transfected into mouse mesenchymal stem cells. Protein expression in the culture supernatant was confirmed by Western blotting (sample 4). The plasmid DNA pCAGGS-XhoI-A-XhoI was used for introduction of the gene into 58 fertilized mouse eggs. These were then implanted into surrogate mouse mothers. A section of tail tissue was cut from 20 of the resulting newborn mice, and DNA was extracted using the DNA mini kit (QIAGEN). PCR was performed to determine whether the samples contained the exogenous gene. Comparison of microarray analyses with mesenchymal stem cells showed homology between the extracellular matrix of the ligament tissues of Wt mice (sample 3), the ligament tissues of mice transgenic for A (sample 2), and mesenchymal stem cell-derived ligament-like tissue.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from cells using an AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
Label Cy3
Label protocol cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray Kit; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Description Sample 3
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with Bioconductor.
 
Submission date Jan 23, 2012
Last update date Mar 31, 2013
Contact name Michiyo Tsuru
E-mail(s) michiyo@med.kurume-u.ac.jp
Phone 81-942-31-7568
Organization name Kurume Universuty
Department Orthopardic Surgery
Street address 67 Asahimachi
City Kurume
State/province Fukuoka
ZIP/Postal code 830-0011
Country Japan
 
Platform ID GPL11202
Series (1)
GSE35269 New protein from an unexpected ligament

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal (non-log scaled)
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_55_P2116608 57.12156 A
A_55_P2073489 712.579625 P
A_52_P229709 4462.08175 P
A_55_P2092526 1108.342425 P
A_55_P2048358 6.6020345 A
A_55_P2109122 24702.515 P
A_55_P2032147 1699.809425 P
A_55_P1985351 5.9060505 A
A_55_P2145838 217.894115 P
A_51_P163444 1363.583384 P
A_55_P2166688 5713.4865 P
A_55_P2230663 16.8426825 A
A_55_P2195172 7.80874375 A
A_55_P1953663 5.664697 A
A_55_P2135730 6.2345195 A
A_51_P174143 6.088748 A
A_51_P419971 3500.926 P
A_55_P1967880 2482.427075 P
A_55_P2364315 94.8739275 P
A_51_P154780 90.6372325 P

Total number of rows: 39429

Table truncated, full table size 1007 Kbytes.




Supplementary file Size Download File type/resource
GSM864797.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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