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Sample GSM1076023 Query DataSets for GSM1076023
Status Public on Apr 01, 2014
Title Mouse622_Cyclosporin_STW
Sample type RNA
 
Source name Mouse622 Liver cells
Organism Mus musculus
Characteristics strain: C57Bl/6
gender: male
age: six-weeks-old
treatment: Cyclosporin
classification: NGTXC
mouse number: 622
tissue: liver
Treatment protocol For the chemicals used in this study, appropriate dosages were derived from previously performed dose range finding (DRF) studies (2-AAF, Phe, CsA, DEHP, DES, E2, PBB, Res, WY, D-man (van Kreijl et al. 2001; de Vries et al. 1997)) or if not known yet, identified by performing additional 28-day DRF studies prior to the short-term exposure studies (see supplemental information 1 for DRF studies using AFB1, CPPD, BPA, DIDP, SD and TBTO). In short, eight to ten weeks old male C57BL/6J mice (n = 10 per group) were exposed to chemicals, using multiple dosages based on literature or expert advice. Body weight dynamics during the first week and over the full 28-day exposure were monitored to extract suitable (non- or slightly cytotoxic) doses (Supplemental information 1). If body weight dynamics were not conclusive, the liver was studied macroscopically (data not shown). Exposure through feed was continuously during the experiment, application using i.p. injection occurred at day 0, 3 and 6 (autopsy on day 7) and exposure using gavage at day 0, 2, 4 and 6 (autopsy on day 7). Body weights were recorded during this 7-day exposure period (Supplemental information 2). Comparison of different control groups (gavage, i.p. injection or feed) showed no significant differential effect on transcriptional levels (Luijten et al. in preparation), hence only food administrated control samples were implemented in this study
Growth protocol Six-week-old male WT mice (C57BL/6J, n=4 per group) were acclimated for 2 weeks and subsequently treated for 7 days with a GTXC, NGTXC or NC through feed, gavage or i.p. injection. From the day of weaning, the health status of the mice was monitored daily and mice were weighed weekly starting at acclimation. Animals were kept in the same stringently controlled (specific pathogen-free, spf) environment, fed ad libitum and kept under a normal day/night rhythm. After 7 days of exposure, mice were sacrificed at a fixed time of the day. During autopsy, several organs (including the liver), were isolated and stored according to protocol using RNAlater (Qiagen, Valencia, CA, USA).
Extracted molecule total RNA
Extraction protocol Hepatic total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA, USA) and the QIAcube (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. All samples passed RNA quality control using capillary gel electrophoresis (RIN > 7.6) (Bioanalyzer 2100; Agilent Technologies, Amstelveen, the Netherlands). The same total RNA isolates as used for mRNA were used for isolation of microRNAs. MicroRNA profiling was performed as previously described (Pothof et al. 2009).
Label biotin
Label protocol MRNA was amplified and labeled with the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit and GeneChip Expression 3'-Amplification Reagents For IVT Labeling according to the manufacturer’s instructions (Eukaryotic Sample and Array Processing 701025 Rev.5; Affymetrix Inc., Santa Clara, CA, USA).
 
Hybridization protocol Amplified materials were hybridized to Mouse Genome 430 2.0 Array for 16 hours at 45°C, subsequently washed and stained with the EukGE-WS2v5_450 protocol
Scan protocol Samples were finally scanned using the GeneChip Scanner 3000-7G (Affymetrix Inc., Santa Clara, CA, USA). Image generation and feature extraction were performed using Affymetrix GCOS Software v1.4.0.036.
Description Quality Control: Approved
Data processing Quality control and correction (correcting significant hybridization and experimental blocking effects), annotation, RMA normalization and subsequent data analysis was performed as previously described (Schaap et al. 2012). Only the annotated Entrez genes were used for further analysis. Functional genomics analyses, using the top 1000 FDR-ranked genes, were performed using Metacore (version 6.11 build 41105, GeneGo Inc. St. Joseph, MI, USA) to assess the biological response upon each chemical exposure
 
Submission date Feb 01, 2013
Last update date Apr 01, 2014
Contact name Joost Melis
E-mail(s) j.p.m.melis@lumc.nl
Organization name Leiden University Medical Center
Department Toxicogenetics
Street address Postbus 9600
City Leiden
ZIP/Postal code 2300 RC
Country Netherlands
 
Platform ID GPL16582
Series (1)
GSE43977 MicroRNA and mRNA biomarkers for short-term in vivo genotoxic and non-genotoxic carcinogen classification

Data table header descriptions
ID_REF
VALUE RMA-signal intensity (log2 scale)

Data table
ID_REF VALUE
100008567_atm 3.380402279
100009600_atd 3.715827608
100012_atd 2.065887971
100017_atd 6.014175859
100019_atd 4.993305069
100034251_atd 8.000736528
100034360_atm 2.468292091
100034675_atm 2.383024456
100034739_atm 2.937888826
100034748_atm 2.715489878
100036520_atm 2.518009226
100036521_atd 7.076088766
100036523_atm 3.400240415
100036525_atm 2.965429236
100036528_atm 1.994447387
100036529_atm 4.659282554
100036534_atm 2.279011016
100036537_atm 2.288728031
100036539_atm 2.428745944
100036541_atm 2.621238597

Total number of rows: 35283

Table truncated, full table size 782 Kbytes.




Supplementary file Size Download File type/resource
GSM1076023_STW_liver_622.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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