|
| Status |
Public on Aug 18, 2014 |
| Title |
ETH_rep1 |
| Sample type |
protein |
| |
|
| Source name |
liver tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)
gender: male
tissue: liver
treatment_agent: Ethionine
treatment_name: Treatment
treatment_type: gastric gavage
treatment_duration: 14 days
treatment_dose [mg/kg/d]: 200
control_group: 5
|
| Treatment protocol |
Animals (8–10 weeks old) were assigned to dose groups (five rats/group) by weight using a weight stratification-based computer program. Substances were administered by gastric gavage for up to 14 days (in a volume of 5 ml/kg body weight/day) based on the group mean weekly body weight for each dose group.
|
| Growth protocol |
Male Wistar Hanover rats (Crl:WI[Gl/BRL/Han]IGS BR) from Charles River Laboratories, Inc. (Raleigh, NC) were maintained on certified rodent chow (Certified Rodent Diet 5200; Purina Mills, St. Louis, MO) ad libitum in individual suspended stainless steel wire-mesh cages. The animals were kept under controlled temperature (18–26°C), humidity (30–70%), and lighting (12 h light/dark cycle) and were acclimated for a minimum of 6 days.
|
| Extracted molecule |
protein |
| Extraction protocol |
Frozen liver tissue was grinded using a ball mill (Mikro-Dismembrator U; Sartorius, Goettingen, Germany). Tissue lysates were generated under denaturing conditions by adding a 8-fold excess (vol/wt) of CeLyA Lysis Buffer CLB1 (Zeptosens).
|
| Label |
Alexa647,Cy5
|
| Label protocol |
Fluorescence signal was generated using Alexa647-/Cy5-labeled anti-species secondary antibodies (Invitrogen, Darmstadt, Germany); details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).
|
| |
|
| Hybridization protocol |
Detection of proteins and protein modifications was performed using a direct two-step immunoassay using specific primary antibodies; details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).
|
| Scan protocol |
Images of the microarrays were taken using the ZeptoREADER microarray imager (Zeptosens), and image analysis was performed using the ZeptoVIEW Pro 3.1 software package (Zeptosens). Signal intensity for each spot was determined as background-corrected mean intensity with the local background subtracted from the spot intensity; the determined values were referenced against adjacent reference spots as implemented in the software package giving referenced fluorescence intensity.
|
| Data processing |
The blank-corrected normalized relative fluorescence intensities (RFI) were for each analyte centered to the median signal level observed for the corresponding control samples and then log2-transformed. Measurements for which the background noise (i.e., signal of secondary antibody) was higher than the combined foreground and background signal (i.e., signal of primary and secondary antibody) were treated as missing values (<1%) and imputed using the k-Nearest-Neighbor (kNN) algorithm.
|
| |
|
| Submission date |
Dec 06, 2013 |
| Last update date |
Aug 18, 2014 |
| Contact name |
Jonathan Moggs |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis
|
| Street address |
Fabrikstrasse 2
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17787 |
| Series (3) |
| GSE53084 |
Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (protein) |
| GSE53085 |
Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat |
| GSE68387 |
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment |
|
