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Sample GSM516388 Query DataSets for GSM516388
Status Public on Nov 21, 2011
Title control 0 h replicate 3
Sample type RNA
 
Source name control
Organism Rattus norvegicus
Characteristics age: 0h
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 0 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 944.88567
113882 32.3352
113886 1362.42495
113892 6.64371
113893 70.30208
113894 2612.6845
113898 2085.06288
113900 395.49439
113901 45.02564
113902 33.58854
113906 1715.03585
113907 131.4797
113910 56.97502
113911 97.00918
113912 489.43875
113914 47.21492
113917 104.02628
113918 60.39953
113919 31.5035
113922 4588.20676

Total number of rows: 21334

Table truncated, full table size 339 Kbytes.




Supplementary file Size Download File type/resource
GSM516388.CEL.gz 22.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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