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Sample GSM1377694 Query DataSets for GSM1377694
Status Public on Jun 01, 2014
Title Hyperglycemic 16 week old NOD PLN - sample 1
Sample type RNA
 
Channel 1
Source name pancreatic lymph nodes
Organism Mus musculus
Characteristics strain: NOD
age: 16 weeks old
Sex: female
glycemic state: hyperglycemic (blood glucose >500 mg/dl)
Treatment protocol pancreatic lymph node tissues were extracted from mice and homogenized in Trizol Reagent.
Growth protocol NOD 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 Mini Kit.
Label Cy5
Label protocol 1 ug 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 lymph nodes (pool of 2 individuals)
Organism Mus musculus
Characteristics strain: NOD
age: 16 weeks old
Sex: female
glycemic state: euglycemic (blood glucose <200 mg/dl)
Treatment protocol pancreatic lymph node tissues were extracted from mice and homogenized in Trizol Reagent.
Growth protocol NOD 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 Mini Kit.
Label Cy3
Label protocol 1 ug 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.
Description Gene expression in the pancreatic lymph node of a hyperglycemic 16-week-old NOD mice compared to that of euglycemic age-matched NOD mice - sample 1
Data processing Data were processed using Genespring 11.5. Samples were filtered for detected entities.
 
Submission date May 01, 2014
Last update date Jun 01, 2014
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)
GSE57237 Gene expression in the pancreatic lymph nodes (PLN) of hyperglycemic 16-week-old Non-Obese Diabetic (NOD) mice compared to expression the PLN of euglycemic 16-week-old NOD mice.

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of Cy5/Cy3 representing Hyperglycemic NOD/Euglycemic NOD controls

Data table
ID_REF VALUE
GE_BrightCorner 1.7380838
A_51_P331831 -1.1484241
A_52_P682382 -1.0017586
A_51_P414661 -0.10273939
A_52_P103628 -0.14891143
A_51_P291339 0.21401785
A_51_P432538 -0.28371337
A_51_P488211 -0.42248428
A_51_P131025 0.56105614
(+)E1A_r60_3 2.9970446
A_51_P256202 -0.034584977
A_52_P666646 0.33406729
A_51_P262432 -0.7525309
A_51_P308298 1.2998457
A_51_P389751 -0.17076106
A_52_P925197 0.51650715
A_51_P490023 0.62518585
A_52_P10458 0.06817046
A_51_P476660 1.3782349
A_51_P158538 -1.1292782

Total number of rows: 5098

Table truncated, full table size 119 Kbytes.




Supplementary file Size Download File type/resource
GSM1377694_16wkNOD1.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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