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Sample GSM3030103 Query DataSets for GSM3030103
Status Public on Jun 05, 2018
Title Differentiated stromal viscular cells
Sample type RNA
Source name Differentiated stromal viscular cells
Organism Mus musculus
Characteristics Sex: male
strain: C57/BL
tissue: Adipose tissue
Treatment protocol Epididymal fat from male C57/BL mice were digested with collagenase, and then centrifuged at 9 ×g for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 ×g for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were incubated with differentiation medium containing insulin/dexamethasone/IBMX for 3 day followed by subsequent incubation with DMEM for 2 day. The cells were collected and RNA was extracted.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Fitchburg, WI) following the manufacturer's instructions. The quality of RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The concentration of the RNA solution was determined by NanoView spectrophotometer (General Electric, Boston, MA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 30 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoView spectrophotometer (General Electric).
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome ver.2.0 Microarrays (G2519F #26655) 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 lightly dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in SVC
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_sep09 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Mar 05, 2018
Last update date Jun 05, 2018
Contact name Shigeo Takashima
Organization name Gifu University
Department Life Science Research Center
Street address 1-1 Yanagido
City Gifu city
State/province Gifu
ZIP/Postal code 501-1194
Country Japan
Platform ID GPL11202
Series (1)
GSE111399 Characteristics of differentiated newly identified adipose precursor cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 0.0821414
DarkCorner -0.22875261
A_55_P1989846 0.5587039
A_55_P1991598 -0.31148815
A_55_P2022211 -0.55479574
A_55_P1980764 -0.41784143
A_55_P1964375 0.5610194
A_51_P128876 0.5124979
A_55_P2121042 -0.22625303
A_52_P219230 2.3899064
A_51_P207591 1.730902
A_55_P2131920 -0.21931553
A_55_P2404223 -0.46203518
A_55_P2101944 -0.76087046
A_52_P358860 -1.8450694
A_51_P119031 -0.003289223
A_51_P309854 -0.23505592
A_51_P343900 0.16794872
A_51_P234359 -0.26499844
A_51_P487813 -1.0337129

Total number of rows: 39485

Table truncated, full table size 963 Kbytes.

Supplementary file Size Download File type/resource
GSM3030103_SVCD.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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