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Sample GSM466149 Query DataSets for GSM466149
Status Public on Oct 18, 2010
Title C0T1_D0-2
Sample type RNA
 
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).
 
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).
 
 
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.
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.
Description no additional information
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.
 
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

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
PRE_VALUE Ratio is calculated as NormCy5/NormCy3 (Relative Intensity, not logged)

Data table
ID_REF VALUE PRE_VALUE
1 NULL NULL
2 NULL NULL
3 NULL NULL
4 NULL NULL
5 NULL NULL
6 NULL NULL
7 NULL NULL
8 NULL NULL
9 NULL NULL
10 NULL NULL
11 NULL NULL
12 -0.0669 0.95471
13 -0.0839 0.94349
14 0.0060 1.0042
15 0.0749 1.0533
16 -0.4792 0.71738
17 NULL NULL
18 -0.0483 0.96707
19 -0.0364 0.97508
20 -0.0240 0.98348

Total number of rows: 45220

Table truncated, full table size 905 Kbytes.




Supplementary file Size Download File type/resource
GSM466149_BAP_D0-2_C0T1_19048_4.txt.gz 559.3 Kb (ftp)(http) TXT
GSM466149_KJ_251486819048_S01_GE2-v5_95_Feb07_1_4.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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