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Sample GSM234806 Query DataSets for GSM234806
Status Public on Oct 06, 2007
Title VPA Treated Rep 2
Sample type RNA
 
Source name VPA treated MC3T3 mice
Organism Mus musculus
Characteristics MC3T3 cell line
Treatment protocol MC3T3 cells were grown in 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.
Growth protocol MC3T3-E1 preosteoblasts were plated at 4x104 cells per well of a 12-well plate and differentiated in Minimal Essential Medium (Invitrogen, Carlsbad, CA) containing 10% FBS (Invitrogen and Cambrex Bioscience/Lonza, Basel. Switzerland), 100 U/ml penicillin, 100 μg/ml streptomycin, 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from MC3T3-E1 osteoblasts with Trizol reagent (Invitrogen).
Label biotin
Label protocol Biotin-labeled cRNA was prepared from each culture according to the Affymetrix protocol. Briefly, RNA was denatured at 70oC with T7-oligo (dT) primer and reverse transcribed using Superscript II at 42oC for 1 hour. Second strand cDNA synthesis was performed by incubating first strand cDNA with Escherichia coli DNA polymerase I, E. coli. DNA ligase, RNase H, and dNTPs for 2 hours at 16oC. Biotin-labeled cRNA was prepared from double-stranded cDNA using the Affymetrix GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA), then purified and fragmented using the Affymetrix Sample Cleanup Module.
 
Hybridization protocol Hybridization of the biotinylated-cRNA to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was performed by the BioMedical Genomics Center’s microarray facility at the University of Minnesota using Affymetrix Genechip® Hybridization Oven 640 and Fluidics Station 450.
Scan protocol Scanning was done with the Affymetrix Genechip® Scanner 3000.
Description Comparison of control mice and mice treated with HDAC inhibitors.
Data processing Raw data measurements were imported into Genedata Expressionist® Refiner (EPro1.0.32) for overall chip hybridization quality assessment, correction and condensation of probe sets intensity values. Robust Multichip Average (RMA) method was applied for global background subtraction and cross array normalization. Processed expression data were imported into Genedata Expressionist Analyst. General assessment of the data distribution was performed with Principle Component Analysis, boxplot and log-log data plots. Following LOESS normalization, differential expression measures were calculated by Welch test comparisons of control DMSO (vehicle) versus each HDAC inhibitor.
 
Submission date Oct 05, 2007
Last update date Aug 28, 2018
Contact name Jennifer J Westendorf
Organization name Mayo Clinic
Street address 200 First Street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL1261
Series (1)
GSE9247 Effect of histone deacetylase inhibitors on osteoblast gene expression
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Significant genes from each comparison were selected using the Benjamini-Hochberg method to control for a maximum false discovery rate (FDR) of 95% or 99% as indicated.
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1425763_x_at 29.476534 A 0.36621094
1427768_s_at 12.374954 A 0.93237305
1417728_at 182.0321 P 7.32E-04
1421879_at 40.68845 P 0.030273438
1426362_at 38.138268 P 7.32E-04
1447616_at 5.3537097 A 0.30371094
1439541_at 39.993202 P 7.32E-04
1416683_at 1035.1432 P 2.44E-04
1431091_at 14.874238 P 0.021484375
1452992_at 166.95709 P 2.44E-04
1451481_s_at 17.095015 A 0.19458008
1424883_s_at 1359.5475 P 2.44E-04
1451380_at 173.86713 P 2.44E-04
1459952_at 16.630922 P 0.014160156
1430816_at 42.374752 P 0.023925781
1448366_at 42.47805 P 0.018554688
1452145_at 142.2986 P 0.005859375
1437327_x_at 258.31818 P 2.44E-04
1458049_at 21.854572 A 0.8503418
1445925_at 14.74118 A 0.96972656

Total number of rows: 45101

Table truncated, full table size 1473 Kbytes.




Supplementary file Size Download File type/resource
GSM234806.CEL.gz 5.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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