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Sample GSM516370 Query DataSets for GSM516370
Status Public on Nov 21, 2011
Title control 8 h replicate 1
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 1
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 728.1504
113882 49.00921
113886 1209.89072
113892 15.45772
113893 53.93326
113894 2562.87337
113898 2225.88769
113900 425.20612
113901 47.25584
113902 27.41011
113906 1600.82392
113907 157.47819
113910 48.3585
113911 108.2236
113912 483.75359
113914 62.67085
113917 95.78419
113918 60.34983
113919 7.78221
113922 4533.01291

Total number of rows: 21334

Table truncated, full table size 339 Kbytes.




Supplementary file Size Download File type/resource
GSM516370.CEL.gz 21.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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