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Sample GSM744137 Query DataSets for GSM744137
Status Public on Jun 01, 2013
Title NP Replicate3 48 Hour Male
Sample type RNA
 
Channel 1
Source name Male zebrafish liver tissue
Organism Danio rerio
Characteristics gender: male
sample type: Nitrophenol-treated liver tissue
tissue: liver
treatment: Nitrophenol
time: 48h
Treatment protocol Male zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.
Growth protocol Zebrafish were maintained at room temperature (26°C + 1°C)
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy5
Label protocol For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
Channel 2
Source name Male and female zebrafish liver tissue
Organism Danio rerio
Characteristics gender: male and female
tissue: liver
treatment: untreated
sample type: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.
Treatment protocol Male zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.
Growth protocol Zebrafish were maintained at room temperature (26°C + 1°C)
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy3
Label protocol For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
 
Hybridization protocol Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_16.5K_oligo_COMP_v3Apx zebrafish oligo probes.
Scan protocol The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
Description Biological replicate 3 of 3: chloroaniline-treated at 48 Hr
Data processing The data were global median normalized. Normalized ratio of means defined by CH1/CH2
 
Submission date Jun 17, 2011
Last update date Jun 01, 2013
Contact name Choong Yong UNG
E-mail(s) matucy@nus.edu.sg
Organization name National University of Singapore
Department Department of Biological Sciences
Street address 14 Science Drive 4
City Singapore
ZIP/Postal code 117543
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE30058 Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with nitrophenol

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of means defined by CH1/CH2

Data table
ID_REF VALUE
5269516 0.013747633
5269517 -0.011827509
5269518 0.097086381
5269519 -0.058463893
5269520 0.099952635
5269521
5269522 0.010834527
5269523 0.729829471
5269524 -0.184956359
5269525 0.05992872
5269526 -0.024887689
5269527 0.244901265
5269528 0.0308679
5269529 0.048594095
5269530 0.611497401
5269531 0.171980846
5269532 -0.063224952
5269533 -0.519863349
5269534 -0.302425592
5269535 0.145602586

Total number of rows: 16512

Table truncated, full table size 322 Kbytes.




Supplementary file Size Download File type/resource
GSM744137_NP3_48h_M.txt.gz 769.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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