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Sample GSM516401 Query DataSets for GSM516401
Status Public on Nov 21, 2011
Title control 8 h replicate 3
Sample type RNA
 
Source name control
Organism Rattus norvegicus
Characteristics age: 8h
tissue: fibroblasts
genotype: c-Myc not 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 control 8 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 1012.4555
113882 40.07552
113886 1426.33967
113892 10.92221
113893 55.58481
113894 3042.88847
113898 2674.15692
113900 549.26975
113901 25.06239
113902 27.89129
113906 1944.7766
113907 123.95019
113910 50.56192
113911 82.77435
113912 363.05474
113914 42.87679
113917 98.62109
113918 63.74399
113919 7.57702
113922 5189.43356

Total number of rows: 21334

Table truncated, full table size 339 Kbytes.




Supplementary file Size Download File type/resource
GSM516401.CEL.gz 22.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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