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Sample GSM1276626 Query DataSets for GSM1276626
Status Public on Nov 28, 2013
Title 4wk old NOD-Replicate 6
Sample type RNA
 
Channel 1
Source name Pancreatic islets
Organism Mus musculus
Characteristics age: 4 week old
Sex: female
strain: NOD/LtJ (NOD)
Treatment protocol pancreatic islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion, and placed in Trizol Reagent.
Growth protocol NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility. All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Micro Kit.
Label Cy5
Label protocol 300 ng of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.
 
Channel 2
Source name Pancreatic Islets (pool of 6 age-matched NOD.B10 mice)
Organism Mus musculus
Characteristics age: 4 week old
Sex: Female
strain: NOD.B10Sn-H2b/J (NOD.B10)
Treatment protocol pancreatic islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion, and placed in Trizol Reagent.
Growth protocol NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility. All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Micro Kit.
Label Cy3
Label protocol 300 ng of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.
 
 
Hybridization protocol Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.
Scan protocol Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)
Description Biological replicate of gene expression in the isolated pancreatic islets of individual 4 week old NOD mice vs. a pool of age-matched NOD.B10 controls
Data processing Data were processed using Genespring 11.5. Samples were filtered for detected entities.
 
Submission date Nov 27, 2013
Last update date Nov 28, 2013
Contact name Linda Yip
Organization name Stanford University
Department Medicine
Lab C.G. Fathman
Street address 269 Campus Drive West, CCSR Building Rm. 2240
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL7202
Series (1)
GSE52815 Gene expression in the isolated islets of 10 day old, 4 wk old, 12 wk old, and 20 wk old Non-Obese Diabetic (NOD) mice compared to healthy age matched control NOD.B10 mice

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of Cy5/Cy3 representing age matched NOD/NOD.B10 controls

Data table
ID_REF VALUE
GE_BrightCorner 0.13308434
A_52_P580582 0.5247893
A_51_P331831 -1.3392457
A_52_P684402 -0.1948061
A_51_P280918 -0.0996466
A_52_P613688 -1.4511341
A_52_P258194 1.3018675
A_52_P214630 0.63442755
A_52_P579519 0.30199152
A_51_P448416 0.27167132
A_51_P215038 -0.40690708
A_52_P427024 -1.0348587
A_52_P669145 -0.21320672
A_51_P318564 0.1958861
A_52_P682382 -0.029563788
A_52_P267543 0.5867596
A_52_P368650 0.82704014
A_51_P414661 0.5547695
A_52_P103628 0.019498767
A_51_P291339 0.3339681

Total number of rows: 22122

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM1276626_4WK-6.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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