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Sample GSM904681 Query DataSets for GSM904681
Status Public on Mar 29, 2012
Title Untreated diabetic-3
Sample type RNA
 
Channel 1
Source name Untreated diabetic
Organism Mus musculus
Characteristics genotype/variation: C57BL/KLS-leprdb/leprdb (db/db)
Treatment protocol Please see our publication Wilson et al PLoS One 2008, PMID: 18648539
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was isolated separately from five heart samples for each condition using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer's instructions. Total RNA was purified using RNeasy columns (Qiagen, Chatsworth, CA). RNA concentration was measured by spectrophotometry, and RNA integrity assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) with 6000 Nano Chips according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to 18S and 28S ribosomal RNA subunits and had a RNA Integrity Number (RIN) greater than six.
Label Cy5
Label protocol Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample. The mouse heart tissue cRNA samples were labeled with Cy5 and the Universal Mouse reference cRNA was labeled with Cy3. The resulting cRNA was purified using an RNeasy kit (Qiagen, Valencia, CA, USA) followed by quantification of the cRNA by spectroscopy using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). 825 ng Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol.
 
Channel 2
Source name Universal control (Stratagene)
Organism Mus musculus
Characteristics reference: Universal mouse reference
Treatment protocol Please see our publication Wilson et al PLoS One 2008, PMID: 18648539
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was isolated separately from five heart samples for each condition using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer's instructions. Total RNA was purified using RNeasy columns (Qiagen, Chatsworth, CA). RNA concentration was measured by spectrophotometry, and RNA integrity assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) with 6000 Nano Chips according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to 18S and 28S ribosomal RNA subunits and had a RNA Integrity Number (RIN) greater than six.
Label Cy3
Label protocol Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample. The mouse heart tissue cRNA samples were labeled with Cy5 and the Universal Mouse reference cRNA was labeled with Cy3. The resulting cRNA was purified using an RNeasy kit (Qiagen, Valencia, CA, USA) followed by quantification of the cRNA by spectroscopy using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). 825 ng Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol.
 
 
Hybridization protocol cRNA was hybridized to 4×44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer's instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.
Scan protocol Slides were washed with Gene Expression Wash Buffer 1 and 2 (Agilent Technologies, Santa Clara, CA) followed by Acetonitrile. A final wash in Stabilization and Drying Solution was performed to prevent Cy-5 degradation by ozone. The array was scanned using an Agilent G2505B DNA microarray scanner under extended Dynamic range.
Data processing The image files were extracted using the Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.
 
Submission date Mar 28, 2012
Last update date Mar 29, 2012
Contact name Kitchener D. Wilson
E-mail(s) kitchwilson@stanford.edu
Organization name Stanford University
Street address S140 Grant Bldg
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL4134
Series (1)
GSE36875 Transcriptome Alteration in the Diabetic Heart by Rosiglitazone: Implications for Cardiovascular Mortality

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.032736184e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 2.329718620e-001
8 0.000000000e+000
9 4.202663665e-002
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 1.051820920e+000
14 1.625897991e+000
15 6.533986362e-002
16 -4.619259194e-001
18 1.152437082e-001
19 1.969923867e-002
20 2.208542101e-001
21 -2.827934178e-001

Total number of rows: 45018

Table truncated, full table size 1018 Kbytes.




Supplementary file Size Download File type/resource
GSM904681_Ag0822single5u100pct_251486814251_S01_GE2-v5_95_Feb07_1_3_db-c.txt.gz 15.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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