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Sample GSM253555 Query DataSets for GSM253555
Status Public on Jan 10, 2008
Title Con14
Sample type RNA
 
Channel 1
Source name saline_8 hr
Organism Rattus norvegicus
Characteristics Tissue: Testis parenchyma
Age: 90 days
Strain: Sprague-Dawley
Exposure=saline i.p.
Time Post treatment: 8 hr
Method of termination: CO2 asphyxiation
Microarray ID: 251186831793
Hyb Date: 2005-07-05
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from a portion of the right testis (about 30 mg) using the Qiagen RNeasy mini kit (Qiagen, Mississauga, ON) following the manufacturerÆs directions, and quantified using Quant-iT RiboGreen RNA assay kit (Invitrogen, Burlington, ON). Total RNA quality was assessed using the RNA 6000 Nano LabChips with the 2100 Bioanalyzer system (Agilent Technologies Inc., Mississauga, ON, Canada). Only samples with the ratios of 18s/28s ribosomal RNA intensity ratios of between 1.65 and 2.0 were used for microarray analyses.
Label Cy5
Label protocol Individual total RNA samples of testis from each animal or universal rat RNA were labelled with Cyanine 5-CTP or Cyanine 3-CTP, respectively (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc.) following the manufacturerÆs instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ╡g total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl, yielding 25 ~35 ╡g labelled cRNA-target. Three micrograms of labelled cRNA were fragmented at 60║C for 30 min with fragmentation solution.
 
Channel 2
Source name universal rat reference total RNA (Catalog #740200; Stratagene, La Jolla, CA, USA)
Organism Rattus norvegicus
Characteristics Total RNA derived from 14 rat cell lines
Microarray ID: 251186831793
Hyb Date: 2005-07-05
Biomaterial provider Stratagene, La Jolla, CA, USA
Extracted molecule total RNA
Extraction protocol Unknown: Material was purchased as total RNA (universal rat reference total RNA (Catalog #740200; Stratagene, La Jolla, CA, USA))
Label Cy3
Label protocol Individual total RNA samples of testis from each animal or universal rat RNA were labelled with Cyanine 5-CTP or Cyanine 3-CTP, respectively (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc.) following the manufacturerÆs instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ╡g total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl, yielding 25 ~35 ╡g labelled cRNA-target. Three micrograms of labelled cRNA were fragmented at 60║C for 30 min with fragmentation solution.
 
 
Hybridization protocol Cy5- sample cRNA and Cy3-labelled common reference cRNA (rat universal reference total RNA (BD Biosciences Clontech, Palo Alto, CA, USA) were hybridized to Agilent rat oligo microarrays (containing ~20,000 unique 60 mer oligonucleotides; Agilent Tech. Inc.) at 60║C overnight with Agilent hybridization solution and washed according to the Agilent's instructions.
Scan protocol Arrays were scanned on a ScanArray Express (Perkin Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, Inc. El Segundo, CA).
Description MAA_Cont_8_251186831793.txt
Data processing The data were normalized by lowess curve (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002; 30: e15.) using SAS/STAT software, Version 8.2 of the SAS System for Windows (1999 2001 SAS Institute Inc., Cary, NC, USA). Data used to estimate foldchanges were adjusted for variation due to date of hybridization using the least square estimates.
 
Submission date Dec 27, 2007
Last update date Feb 20, 2008
Contact name Mike G Wade
E-mail(s) Mike_Wade@hc-sc.gc.ca
Phone 613 946 5127
Fax 613 957 8800
Organization name Health Canada
Department Environmental Health Science & Research Bureau
Lab Reproductive Toxicology
Street address 50 Columbine Driveway
City Ottawa
State/province Ontario
ZIP/Postal code K1A 0K9
Country Canada
 
Platform ID GPL890
Series (1)
GSE10032 The acute effects of methoxyacetic acid exposure on testis gene expression

Data table header descriptions
ID_REF
VALUE ratio is the normalized log2 ratio (sample/reference), rawCy3 is the raw median signal intensity for the reference, rawCy5 is the raw median signal intensity for the sample, ImageneFlag is the Imagene flag value, BackgroundFlag where 1 indicates if the raw median signal intensity is below the trimmed mean (5%) plus 3 trimmed standard deviations of the negative control spots, ProcessedCy3 is the normalized median signal intensity adjusted for the day of hybridization, ProcessedCy5 is the normalized median signal intensity adjusted for the day of hybridization
Flag flag information; 1 = absent (not more than 3 S.D. above mean background); 0 = present

Data table
ID_REF VALUE Flag
1 2.962402695 0
2 -0.233379204 1
3 -0.02800111 1
4 0.094960561 0
5 -0.499675239 1
6 -0.148849331 1
7 3.513458141 0
8 -0.368548732 1
9 -0.342625478 1
10 0.768105594 0
11 -0.118653557 1
12 0.373783186 1
13 0.935325935 0
14 4.32311776 0
15 -1.049420564 0
16 -0.325698011 1
17 -0.032907723 1
18 -0.5305756 1
19 0.09559025 0
20 1.318544575 0

Total number of rows: 22573

Table truncated, full table size 438 Kbytes.




Supplementary file Size Download File type/resource
GSM253555.txt.gz 589.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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