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Sample GSM290507 Query DataSets for GSM290507
Status Public on May 24, 2008
Title Male Hypox/Female Hypox comparison/Replicate #1
Sample type RNA
 
Channel 1
Source name Frozen adult female rat liver tissue prepared using Trizol
Organism Rattus norvegicus
Characteristics Strain: Fischer 344
Treatment: Hypophysectomy (‘Hypox’)
Sex: female
Tissue: liver
Age: 12 weeks
Extracted molecule total RNA
Extraction protocol Trizol extraction
Label Alexa 555
Label protocol RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
 
Channel 2
Source name Frozen adult male rat liver tissue prepared using Trizol
Organism Rattus norvegicus
Characteristics Strain: Fischer 344
Treatment: Hypophysectomy (‘Hypox’)
Sex: male
Tissue: liver
Age: 12 weeks
Extracted molecule total RNA
Extraction protocol Trizol extraction
Label Alexa 647
Label protocol RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
 
 
Hybridization protocol Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash.
Scan protocol Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).
Description The RNA expression profile for a single male Hypox liver pool and a single female Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox rat liver gene expression.
Data processing LOWESS normalized expression ratios, Rosetta Resolver pipeline
 
Submission date May 21, 2008
Last update date May 23, 2008
Contact name David J. Waxman
E-mail(s) djw@bu.edu
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL4135
Series (1)
GSE11529 Sex-specific early growth hormone response genes in rat liver (Rattus norvegicus)

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
INTENSITY1 Background adjusted Female Hypox value
INTENSITY2 Background adjusted Male Hypox value
PRE_VALUE Normalized ratio (INTENSITY2/INTENSITY1)

Data table
ID_REF VALUE INTENSITY1 INTENSITY2 PRE_VALUE
1 0.09 7118.50 7555.13 1.0613
2 0.31 3.32 4.10 1.2370
3 0.31 3.30 4.08 1.2376
4 0.31 3.28 4.06 1.2381
5 0.31 3.26 4.03 1.2385
6 0.31 3.24 4.01 1.2388
7 0.31 3.22 3.99 1.2389
8 0.31 3.20 3.97 1.2390
9 0.31 3.19 3.95 1.2390
10 0.31 3.17 3.93 1.2388
11 0.31 3.15 3.90 1.2386
12 0.31 3.14 3.88 1.2384
13 0.45 35.27 48.14 1.3648
14 0.06 23.78 24.87 1.0460
15 -0.19 15.99 14.01 0.8759
16 0.32 122.96 152.98 1.2442
17 0.09 4280.45 4564.48 1.0664
18 -0.28 5.59 4.60 0.8236
19 0.13 194.08 212.58 1.0953
20 -0.21 1213.56 1050.53 0.8657

Total number of rows: 45018

Table truncated, full table size 1358 Kbytes.




Supplementary file Size Download File type/resource
GSM290507.txt.gz 12.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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