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Sample GSM516369 Query DataSets for GSM516369
Status Public on Nov 21, 2011
Title OHT treated 24 h replicate 1
Sample type RNA
 
Source name OHT treated
Organism Rattus norvegicus
Characteristics age: 24h
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 24 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 742.37488
113882 34.61156
113886 1201.68478
113892 20.73306
113893 54.37488
113894 2034.6451
113898 1191.95354
113900 70.94774
113901 40.55264
113902 29.15864
113906 1394.27228
113907 151.29056
113910 78.2047
113911 108.84841
113912 568.93767
113914 47.92508
113917 83.85944
113918 42.42363
113919 14.47501
113922 3490.94402

Total number of rows: 21334

Table truncated, full table size 338 Kbytes.




Supplementary file Size Download File type/resource
GSM516369.CEL.gz 22.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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