MAQC rat toxicogenomics samples used in Guo L. et al., Nature Biotechnology, 24(9), 2006.
Treatment protocol
Groups of six 6-week-old Big Blue rats were gavaged with riddelliine (1 mg/kg body weight) or aristolochic acid (10 mg/kg body weight) five times a week for 12 weeks or Big Blue rats were fed a diet of 8% comfrey roots for 12 weeks. The animals were sacrificed after 12 weeks of treatment, and the tissues were isolated, frozen quickly in liquid nitrogen and stored at –80 °C.
Extracted molecule
total RNA
Label
biotin
Label protocol
1 ug of total RNA was processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Rat Whole Genome Bioarray (catalog #300031).
Scan protocol
All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.
Description
The samples were randomly labeled and each test site was provided an aliquot of each sample. To avoid potential confounding factors in experimental implementation, the identity of the RNA samples was kept unknown to the test sites before data were submitted to FDA/NCTR.
Data processing
The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics. These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment. The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background. Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).
Local background subtracted intensity data and median-scaling each array to a median of 1.
Flag_Detection
GEH's original flag information ('Quality_flag') is provided: G = 'Good', L = 'Absent', S = 'Saturated', M = 'Manufacturing Defect', I = 'Irregular Shape', C = 'Contaminated Spot'.
