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Sample GSM1576684 Query DataSets for GSM1576684
Status Public on Jan 06, 2015
Title LVX
Sample type RNA
 
Source name MIN6, trasfected with PLVX-IRES-ZsGreen
Organism Mus musculus
Characteristics cell type: a transgenic C57Bl/6 mouse-derived insulinoma cells
passages: 15-20
cell line: MIN6
treatment: control
Treatment protocol Packaging of pseudotyped recombinant lentivirus was performed by transfection of 293T cells. Briefly, FTO overexpression vector pLVX-IRES-ZsGreen1-FTO or empty vector was ransfected with package vectors pCMV Δ8.91 and pMD.G into 293T cells using Lipofectamine 2000. Lentivirus in the culture media was harvested at 72 h and filtered through a 0.45 µm low protein binding polysulfonic filter. The virus was frozen and kept in -70 °C freezer for future use. For virus infection, MIN6 cells were plated into 6-cm dishes in advance and cultured for nearly 18 hours with about 50% confluence before transduction. The lentivirus suspension in the presence of 8 µg/ml polybrene was added to the cells. After transduction for 48 h, green fluorescence was observed to indicate the transduction efficiency.
Growth protocol MIN6 cells were cultured in DMEM medium with 15% fetal bovine serum, 100 U/ml penicillin, 100 µg/ml streptomycin and 50 µM β-mercaptoethanol in 5% CO2 /95% air in a humidified atmosphere at 37 °C
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacture’s procedure.
Label Cy3-UTP
Label protocol Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.
 
Hybridization protocol The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.
Scan protocol The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)
Description Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis
Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5). GO analysis and Pathway analysis were performed in the standard enrichment computation method
 
Submission date Jan 05, 2015
Last update date Jan 06, 2015
Contact name Hong-Qi Fan
Organization name The First Affiliated Hospital of Nanjing Medical University
Department Department of Endocrinology
Street address 300 Guangzhou RD
City Nanjing
State/province Jiangsu
ZIP/Postal code 210029
Country China
 
Platform ID GPL11202
Series (1)
GSE64668 Effect of FTO (fat mass and obesity-associated) overexpression on gene expression profiling in beta cells

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
A_55_P1989846 11.090841
A_55_P2022211 7.9650974
A_55_P1980764 5.3188715
A_55_P1964375 12.768208
A_51_P128876 9.297739
A_55_P2121042 6.034527
A_52_P219230 4.964059
A_51_P207591 5.4050446
A_55_P2131920 3.9724455
A_55_P2404223 9.42328
A_55_P2101944 13.772407
A_52_P358860 10.776134
A_51_P119031 11.998089
A_51_P309854 10.881294
A_51_P343900 14.250828
A_51_P234359 15.164574
A_51_P487813 13.556941
A_52_P613977 13.706402
A_55_P1957209 3.9078732
A_52_P549166 5.044442

Total number of rows: 33870

Table truncated, full table size 767 Kbytes.




Supplementary file Size Download File type/resource
GSM1576684_LVX.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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