|
| Status |
Public on Aug 18, 2014 |
| Title |
Kidney_S011127-097_Neomycin_56 mg/kg_0.25d |
| Sample type |
RNA |
| |
|
| Source name |
Kidney, Neomycin, 0.25d
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley, CD-IGS
tissue: Kidney
compound: Neomycin
dose: 56 mg/kg
time: 0.25 d
vehicle: Corn Oil
route: Oral Gavage
Sex: Male
rna extraction date: 2002-01-21
hybridization date: 2002-01-28
|
| Treatment protocol |
The 0.25 and 1-day time points were harvested starting at 1:00 p.m. and completed within 1–2 h, whereas the 3 and 5-day time points were harvested starting at 7:00 a.m. and completed within 2–4 h; all harvests used an appropriately staggered schedule so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.
|
| Growth protocol |
Male Sprague–Dawley (Crl:CD® (SD)|GS BR) rats(aged 6–8 weeks) were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22±3 ◦C; humidity 30–70%; 12-h light:12-h dark cycle per day, 6:00 a.m.–6:00 p.m.) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Poly A(+) RNA was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I (Roche, Basel, Switzerland), concentrated by ethanol precipitation, resuspend in 7 ul DEPC-treated water, quantified by ribogreen fluorescence using Wallac Victor2 fluorometer (Perkin Elmer, Fremont CA) and transcribed to cDNA
|
| Label |
Biotin
|
| Label protocol |
The methods used for cRNA preparation are described in the CodeLinkTM manual v2.1 as supplied by Amersham Biosciences using the Qiagen BioRobot 9604 (Valencia, CA).
|
| |
|
| Hybridization protocol |
Ten micrograms of the fragmented cRNA was hybridized to each Uniset Rat I Expression BioArray (Amersham Biosciences) for 20 h at 37 ◦C, while shaking at 300 rpm.
|
| Scan protocol |
All processed slides were scanned using the Axon GenePix Scanner (Axon Instrument, Union City, CA) with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10_m. The data were analyzed using the CodeLinkTM Expression Analysis Software Version 2.2.25 (Amersham Biosciences).
|
| Description |
Complete Drug Matrix dataset for primary rat hepatocytes; more details can be found at http://cebs.niehs.nih.gov/ under accession number 004-00008-0000-000-2
|
| Data processing |
Data was extracted from the Probe Value column of background-subtracted files, and quantile-normalized, without baseline transformation in GeneSpring GX 11.5.1. Data artifacts (probes with -2 as the probe value) were removed (set to empty) before normalization. Probe values that were blank were left blank.
|
| |
|
| Submission date |
Jul 30, 2014 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Scott Auerbach |
| E-mail(s) |
AuerbachS@niehs.nih.gov
|
| Organization name |
Division of the National Toxicology Program at NIEHS
|
| Street address |
111 TW Alexander Drive
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL5424 |
| Series (2) |
| GSE59913 |
Exposure of rat to a variety of toxicants, kidney assayed by CodeLink microarray |
| GSE59927 |
Drug Matrix Data - CodeLink Arrays |
|
