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Sample GSM735918 Query DataSets for GSM735918
Status Public on Nov 01, 2011
Title Control at Day 8, biological rep 4
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)

Data table header descriptions
ID_REF
VALUE PLIER normalized signal intensity

Data table
ID_REF VALUE
10701620 0
10701630 0.040795803
10701632 -0.04174757
10701636 0.002851963
10701643 0.03775406
10701648 -0.07651901
10701654 0.098921776
10701663 -0.15179253
10701666 0
10701668 -5.38E-04
10701671 0
10701674 0.036677837
10701679 -0.016858578
10701684 -0.007992268
10701689 -0.0884738
10701691 0.0388155
10701697 -0.13224936
10701699 -0.147192
10701709 0.04113388
10701714 0.043762207

Total number of rows: 27342

Table truncated, full table size 541 Kbytes.




Supplementary file Size Download File type/resource
GSM735918.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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