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Sample GSM1006480 Query DataSets for GSM1006480
Status Public on Feb 28, 2013
Title Mouse liver PB vs. Control 1.5X cDNA 8
Sample type RNA
 
Channel 1
Source name Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 2.2
Organism Mus musculus
Characteristics age: 42 days
gender: male
strain: B6C3F1
organ: liver
exposure: Phenobarbital
cdna input: 1.5X
Treatment protocol Mice were exposed to PB in drinking water (or drinking water alone) for ~4 weeks
Growth protocol 16-year-old FFPE liver tissue blocks were used
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen FFPE Rneasy kit; cDNA was synthesized using the WTA2 kit (Sigma)
Label Cy5
Label protocol cDNA was labeled using the KREAtech ULS genomic DNA labeling kit (Agilent)
 
Channel 2
Source name Control mouse liver, 1.5X cDNA input, replicate 2.2
Organism Mus musculus
Characteristics age: 42 days
gender: male
strain: B6C3F1
organ: liver
exposure: none
cdna input: 1.5X
Treatment protocol Mice were exposed to PB in drinking water (or drinking water alone) for ~4 weeks
Growth protocol 16-year-old FFPE liver tissue blocks were used
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen FFPE Rneasy kit; cDNA was synthesized using the WTA2 kit (Sigma)
Label Cy3
Label protocol cDNA was labeled using the KREAtech ULS genomic DNA labeling kit (Agilent)
 
 
Hybridization protocol 1X (samples 1-8) or 1.5X (samples 9-16) cDNA was blocked with Agilent CGH-block and GE-blocking agent and hybridized to Agilent SurePrint GE 8x60 1.5 Mouse microarrays for 17 hours at 65C at 20rpm
Scan protocol Arrays were washed and scanned on an Agilent G2505B Scanner according to manufacturer’s recommendations. 
Description Pos_2_4_Dye_Cy5_Sample_53
Pos_2_4_Dye_Cy3_Sample_38
Data processing Agilent FE software, version 11 (one color protocol: GE1_1100_Jul11, or two-color protocol: GE2_1100_Jul11).
 
Submission date Sep 19, 2012
Last update date Feb 28, 2013
Contact name Anna Francina Jackson
E-mail(s) francina.jackson@hc-sc.gc.ca
Organization name Health Canada
Department Environmental Health Center
Lab Dr. Carole Yauk
Street address 50 Colombine Drive, Tunney's Pasture
City Ottawa
State/province Ontario
ZIP/Postal code K1A 0K9
Country Canada
 
Platform ID GPL13912
Series (1)
GSE40990 Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

Data table header descriptions
ID_REF
VALUE normalized log10 ratio test/reference

Data table
ID_REF VALUE
1 -1.492086372e-001
2 0.000000000e+000
3 6.991944716e-001
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 -1.752624714e-001
8 -3.194312422e-001
9 0.000000000e+000
10 0.000000000e+000
11 3.662513068e-001
12 0.000000000e+000
13 -1.682200529e-001
14 -4.515394753e-001
15 -2.351735237e-001
16 0.000000000e+000
17 -2.152678242e-001
18 0.000000000e+000
19 -5.376576973e-002
20 -5.922358884e-001

Total number of rows: 62976

Table truncated, full table size 1435 Kbytes.




Supplementary file Size Download File type/resource
GSM1006480_252800512587_201205251046_S01_GE2_1100_Jul11_2_4.txt.gz 5.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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