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Sample GSM2460213 Query DataSets for GSM2460213
Status Public on Jan 17, 2017
Title Mixture Replicate 2
Sample type RNA
 
Channel 1
Source name Liver tissue exposed to a mixture of EE2/ZM
Organism Pimephales promelas
Characteristics tissue: Liver
Sex: male
treatment: mixture of estrogen EE2 and the anti-estrogen ZM
Treatment protocol Exposed to estrogen EE2, a mixture of EE2 and the anti-estrogen ZM, or solvent control.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from FHM livers with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
Label Cy5
Label protocol Array hybridizations were performed using a reference design and Agilent standard protocol. The liver samples were labeled with Cy5, while the reference sample was labeled with Cy3.
 
Channel 2
Source name Reference sample
Organism Pimephales promelas
Characteristics tissue: Pool of liver, gonad, and brain
Sex: Pooled male and female
Treatment protocol Exposed to estrogen EE2, a mixture of EE2 and the anti-estrogen ZM, or solvent control.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from FHM livers with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
Label Cy3
Label protocol Array hybridizations were performed using a reference design and Agilent standard protocol. The liver samples were labeled with Cy5, while the reference sample was labeled with Cy3.
 
 
Hybridization protocol Hybridization was performed following the standard Agilent protocol.
Scan protocol Arrays were scanned with Agilent scanner.
Description MIX-108
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.
Data processing Microarray image processing and data pre-processing were performed using Agilent’s Feature Extraction software v 9.5. In brief, log2 transformed signal ratio between the experimental channel and the reference channel was calculated for each spot, followed by within-array LOWESS transformation and between array scale normalization on median intensities (Zahurak, 2007). Two-way ANOVA was performed on the log2 transformed signal ratios of each probe individually, followed by Tukey-HSD pair-wise comparisons to determine genes whose expression was significantly regulated by the treatments.
 
Submission date Jan 16, 2017
Last update date Jan 17, 2017
Contact name Natalia Vinas
E-mail(s) [email protected], [email protected]
Phone 6016343764
Organization name Mississippi State University
Street address 3909 Halls Ferry Rd
City Vicksburg
State/province MS
ZIP/Postal code 39180
Country USA
 
Platform ID GPL7282
Series (1)
GSE93663 Fathead minnow liver samples: control, EE2 and EE2/zm

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 2.91E-01
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 5.03E-01
13 0.00E+00
14 0.00E+00
15 -2.87E-01
16 0.00E+00
17 -2.42E-01
18 8.04E-01
19 2.11E-01
20 -5.68E-01

Total number of rows: 44407

Table truncated, full table size 658 Kbytes.




Supplementary file Size Download File type/resource
GSM2460213_MIX-108.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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