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Sample GSM735921 Query DataSets for GSM735921
Status Public on Nov 01, 2011
Title Control at Day 29, biological rep 1
Sample type RNA
 
Source name Control at Day 29
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: liver
treatment: control
time: day 29
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 29.
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 0.08279514
10701630 -0.004193306
10701632 -0.029613018
10701636 0.071640015
10701643 0.19409943
10701648 0.08302498
10701654 0.05721569
10701663 -0.5870662
10701666 0.01656437
10701668 0.10058117
10701671 -0.09717035
10701674 -0.055259228
10701679 0.028362751
10701684 0.107237816
10701689 -0.04675436
10701691 0.35318184
10701697 -0.028725624
10701699 -0.4394169
10701709 0.029040337
10701714 0.10276461

Total number of rows: 27342

Table truncated, full table size 538 Kbytes.




Supplementary file Size Download File type/resource
GSM735921.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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