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Status |
Public on Oct 18, 2010 |
Title |
C0T1_D0-2 |
Sample type |
RNA |
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Channel 1 |
Source name |
Total RNA, mouse liver
|
Organism |
Mus musculus |
Characteristics |
exposure: Control time post exposure: 4hrs microarray slide block: 2 microarray barcode: 19048_4 gender: Male age: 27-30 days strain: B6C3F1 tissue: Median liver lobe
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada). RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).
|
Label |
Cy5
|
Label protocol |
Double-stranded cDNA and cyanine labelled cRNA was synthesized according using Agilent Linear Amplification Kits. Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen).
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Channel 2 |
Source name |
universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)
|
Organism |
Mus musculus |
Characteristics |
reference: Total RNA derived from 11 mouse cell lines microarray slide block: 2 microarray barcode: 19048_4
|
Extracted molecule |
total RNA |
Extraction protocol |
Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))
|
Label |
Cy3
|
Label protocol |
Double-stranded cDNA and cyanine labelled cRNA was synthesized according using Agilent Linear Amplification Kits. Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen).
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Hybridization protocol |
Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed according to the manufacturer’s specifications.
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Scan protocol |
Arrays were scanned on an Agilent G2505B scanner using default settings at 5mm, PMT 100%, extended dynamic range 0.1. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.
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Description |
no additional information
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Data processing |
The median signal intensity of each microarray sample was used. Technical replicates were not averaged. Data for each probe was flagged (flag=1) if the median signal intensity for that probe was less than the mean of the negative controls ((-)3xSLv1) plus three standard deviations. BAP_*.txt processed data files: RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls.) Ratio is calculated as NormCy5/NormCy3 (Relative Intensity, not logged.) KJ_*.txt files are raw data files.
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Submission date |
Oct 28, 2009 |
Last update date |
Oct 18, 2010 |
Contact name |
Andrew Williams |
Organization name |
Health Canada
|
Street address |
50 Columbine
|
City |
Ottawa |
State/province |
ON |
ZIP/Postal code |
K1A OK9 |
Country |
Canada |
|
|
Platform ID |
GPL4134 |
Series (2) |
GSE18789 |
mRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Agilent gene expression array] |
GSE18841 |
Adult mouse liver following benzo(a)pyrene (BaP) treatment: miRNA and mRNa profiling |
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