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Sample GSM516393 Query DataSets for GSM516393
Status Public on Nov 21, 2011
Title OHT treated 5 h replicate 3
Sample type RNA
 
Source name OHT treated
Organism Rattus norvegicus
Characteristics age: 5h
tissue: fibroblasts
genotype: c-Myc active
Treatment protocol Cells were plated at a density of 20% confluence 24 h prior to the addition of OHT (248 nM; for treated cells) or an equal volume of ethanol (for mock-treated cells).
Growth protocol HOMycER12 cells were cultured, under exponential growth conditions, in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% calf serum (Hyclone) at 37°C and 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using the TRIZOL® reagent (Invitrogen) according to the manufacturer’s protocol.
Label biotin
Label protocol RNA was converted into biotinylated single stranded cDNA as described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
 
Hybridization protocol As described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
Scan protocol Scanning was carried on a GCS3000 scanner
Description OHT treated 5 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt
Data processing The Probe Logarithmic Intensity Error (PLIER) algorithm, from the Affymetrix Power Tools (APT) software package, was used to generate gene and exon expression scores. Probes were filtered and remapped to rat genes with Entrez ID according to the tables provided by the Microarray Laboratory of the Molecular and Behavioral Neuroscience Institute, University of Michigan.
 
Submission date Feb 26, 2010
Last update date Nov 21, 2011
Contact name Chui Sun Yap
E-mail(s) chuisunyap@gmail.com
Organization name Duke-NUS
Street address 8, College Road
City Singapore
ZIP/Postal code 169857
Country Singapore
 
Platform ID GPL10112
Series (1)
GSE20550 A high resolution analyis of c-Myc-regulated gene expression dynamics.

Data table header descriptions
ID_REF
VALUE Quantile normalized gene level expression values from PLIER.

Data table
ID_REF VALUE
112400 840.55237
113882 30.78042
113886 1280.97381
113892 17.41289
113893 46.50909
113894 1898.35079
113898 2537.46232
113900 334.97065
113901 35.91176
113902 32.63339
113906 1589.83391
113907 118.33789
113910 62.80248
113911 85.96216
113912 398.64178
113914 44.88179
113917 96.48456
113918 59.28367
113919 4.45243
113922 5053.71315

Total number of rows: 21334

Table truncated, full table size 339 Kbytes.




Supplementary file Size Download File type/resource
GSM516393.CEL.gz 23.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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