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Sample GSM2232967 Query DataSets for GSM2232967
Status Public on Nov 05, 2019
Title Control_M2 (IM study)
Sample type RNA
 
Source name 4 months old zebrafish liver
Organism Danio rerio
Characteristics tissue: liver
age: 4 months old
gender: male
treatment: H2O
Treatment protocol Imatinib mesylate (sc-202180A, Santa Cruz Biotechnology) was diluted in the clean recirculation system water to final concentrations of the exposure of 0.01 µg/L (C1) and 1.0 µg/L (C2). The control group was grown in the recirculation system water alone. All of the treatments, including the controls, were carried out in duplicate. The experiment was performed under the semistatic conditions with a complete renewal of exposure medium every three days. At the age of 4 months, part of F1 fish was sampled for gene expression analyses.
Growth protocol The wild time (AB line) of zebrafish (Danio rerio) originated and was cultured at the Department of Aquaculture of Szent István University (Hungary). Prior to the study, the parent generation was maintained in a recirculation system that allowed continuous flow of water (ZebTec; Tecniplast Inc.) under a light regime of 14 h light/ 10 h dark. The parameters of the recirculation system water were as follows: temperature, 25 ±0.5 °C; pH, 7.4 ±0.2; and conductivity, 525 ±50 µS. During the study period, the zebrafish were maintained at 24 °C to 26 °C under a light regime of 14 h light/ 10 h dark. Fish were fed twice a day with SDS Small Gran granulated feed and twice a week, with Artemia. The animal protocol was approved by the Hungarian Animal Welfare Law .
Extracted molecule total RNA
Extraction protocol The RNA was isolated by Direct-zol RNA Miniprep (ZymoResearch) from liver of 6 individuals liver per exposure point from each of the two replicates. After RNA quality and quantity evaluation (Agilent Bioanalyzer, RNA 6000 Nano Kit, Eukaryote Assay), RNA from 1-3 individuals from same treatment, replicate and gender was pooled, DNase treated (Invitrogen DNaseI; 0.2 U/µg RNA) in 45 μl reactions and subsequently purified using RNeasy Mini Elute kit (Qiagen). Purified RNA was checked for integrity and quantity by Bioanalyzer.
Label Cy3
Label protocol Labelling, hybridization and scanning were performed by the IMGM (Germany). The total RNA was labelled with Cy-3 using Low Input Quick-Amp Labeling Kit One-Color (Agilent technologies) following manufacturers protocol
 
Hybridization protocol Hybridizations and washes were performed using Gene Expression Hybridization Kit (Agilent Technologies) following manufactures protocol
Scan protocol Hybridized slides were scanned on Agilent DNA Microarray Scanner and signals were extracted and quality control was performed using Feature Extraction 10.7.3.1 Software (Agilent Technologies).
Description pool of 2 individuals
Data processing Microarray data analysis was performed in R environment (version 2.15.1) using Bioconductor’s libraries limma and vsn.
 
Submission date Jul 14, 2016
Last update date Nov 05, 2019
Contact name Spela Baebler
E-mail(s) spela.baebler@nib.si
Organization name National Institute of Biology
Department Department of Biotechnology and Systems Biology
Street address Vecna pot 111
City Ljubljana
ZIP/Postal code 1000
Country Slovenia
 
Platform ID GPL14664
Series (1)
GSE84394 Zebrafish liver transcriptome in response to chronic treatment with environmentally relevant concentrations of imatinib mesylate

Data table header descriptions
ID_REF
VALUE log2 normalized intensities

Data table
ID_REF VALUE
(-)3xSLv1 3.158049684
(+)E1A_r60_1 17.91603518
(+)E1A_r60_3 3.248350751
(+)E1A_r60_a104 2.864922634
(+)E1A_r60_a107 5.254943474
(+)E1A_r60_a135 8.155185542
(+)E1A_r60_a20 9.311344568
(+)E1A_r60_a22 10.93514915
(+)E1A_r60_a97 13.49672004
(+)E1A_r60_n11 15.20507522
(+)E1A_r60_n9 16.29875058
(+)eQC-39 2.651483404
(+)eQC-40 3.916148466
(+)eQC-41 3.335051857
(+)eQC-42 4.120122358
A_15_P100008 8.279091083
A_15_P100009 6.104289037
A_15_P100011 8.155185542
A_15_P100012 10.95208389
A_15_P100015 9.559213588

Total number of rows: 43663

Table truncated, full table size 1060 Kbytes.




Supplementary file Size Download File type/resource
GSM2232967_RS-346_0005.txt.gz 9.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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