|
| Status |
Public on Nov 01, 2011 |
| Title |
Control at Day 8, biological rep 6 |
| Sample type |
RNA |
| |
|
| Source name |
Control at Day 8
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: liver
treatment: control
time: day 8
|
| Treatment protocol |
Rats were given once daily with vehicle control (1% methy cellulose in steril water) or 200 mg/kg (low dose) or 2000 mg/kg (ligh dose) PMCol by oral gavage for either 7 days or 28 days, and eutahnized on Day 8 or Day 29. Liver left lobe was cut into ≤ 0.3 cm cubed sections, submerged in RNAlater. refrigerated overnight, and then stored frozen at ≤ -60°C until RNA isolation
|
| Growth protocol |
Male Crl:CD Sprague-Dawley Virus Antibody Free rats (Harlan, Livermore, CA) 6-7 weeks of age were maintained on Purina Certified Rodent Chow 5002 (Richmond, IN) and reverse osmosis purified tap water ad libitum under controlled lighting (12 h light-dark cycle).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using the Ambion RiboPure RNA isolation kit (Applied Biosystems, Life Technologies, Carlsbad, CA) with 1-bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO). Residual genomic DNA was removed using the Ambion TURBO DNA-free kit (Applied Biosystems).
|
| Label |
biotin
|
| Label protocol |
Total RNA (150 ng) from each liver sample was processed to double-stranded cDNA using the Ambion WT Expression kit (Applied Biosystems), followed by a 16-hr in vitro transcription reaction. Second-cycle cDNA was synthesized using 12 µg cRNA, and then 5.5 µg was fragmented and biotin-labeled using the GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Hybridization to GeneChip Rat Gene 1.0 ST Arrays were performed as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay, revision 5
|
| Scan protocol |
hydrization oven 640, GeneChip Fluidics Station 450, GeneChip Scanner 3000 7G, and GeneChip command console software.
|
| Description |
Gene expression data from vehicle control animal sacrificed on Day 8.
|
| Data processing |
MAS5, In addition, the probe logarithmic intensity error (PLIER) method was used to build upon the summarization algorithm provided in Affymetrix® Microarray Suite 5.0 (MAS 5) by taking into account the experimentally validated value of weighting feature intensities to determine an overall probe set summary. GeneSpring GX11.0 software (Agilent Technologies)
|
| |
|
| Submission date |
Jun 01, 2011 |
| Last update date |
Nov 01, 2011 |
| Contact name |
Hanna Hongchin Ng |
| E-mail(s) |
hanna.ng@sri.com
|
| Organization name |
SRI International
|
| Street address |
333 Ravenswood Avenue
|
| City |
Menlo Park |
| State/province |
CA |
| ZIP/Postal code |
94025 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE29673 |
Toxicogenomic Study of Pentamethylchromanol (PMCol) |
|
