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Sample GSM272660 Query DataSets for GSM272660
Status Public on Jun 26, 2008
Title p53-/- TAF6 AS2 3
Sample type RNA
 
Source name HCT-116 p53 -/- cell line
Organism Homo sapiens
Characteristics HCT-116 p53-/- cells + Taf6 RNA oligo
Extracted molecule total RNA
Extraction protocol RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer
Label DIG-UTP
Label protocol Digoxigenin-UTP labeled cRNA was generated and amplified from 2 µg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol(P/N 4365710).
 
Hybridization protocol Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturer’s protocol (P/N 4339627).
Scan protocol image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).
Description TAF6 AS2 treated HCT-116 p53-/- cells
Data processing Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.
 
Submission date Mar 12, 2008
Last update date Jun 20, 2008
Contact name Arndt Benecke
E-mail(s) arndt@ihes.fr
Phone +33160926665
Fax +33160926609
URL http://seg.ihes.fr
Organization name Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS
Department Integrative Biology
Lab Systems Epigenomics
Street address 35 route des Chartres
City Bures-sur-Yvette
ZIP/Postal code 91440
Country France
 
Platform ID GPL1426
Series (1)
GSE10795 p53 independent TAF6delta target genes.

Data table header descriptions
ID_REF
VALUE Mediane Normalized Signal
VAR Coefficient of Variation
A Probability for a gene to be expressed

Data table
ID_REF VALUE VAR A
100002 314.1111 0.0400 1.0000
100003 0.4259 0.6900 0.2417
100027 0.5556 0.5500 0.3880
100036 2.4722 0.1500 1.0000
100037 59.3981 0.0400 1.0000
100039 14.5556 0.0700 1.0000
100043 0.2037 0.9700 0.0202
100044 0.2407 0.7600 0.0227
100045 0.2593 0.6500 0.0211
100051 0.5648 0.4100 0.3768
100052 0.2500 0.8900 0.0520
100057 4.8889 0.0800 1.0000
100058 131.0000 0.0400 1.0000
100060 0.3519 1.1700 0.2429
100062 0.7407 4.1500 0.5149
100064 241.1944 0.0400 1.0000
100079 379.9722 0.0500 1.0000
100089 10.4815 0.0600 1.0000
100093 0.1944 1.3000 0.0484
100095 0.8704 3.0200 0.5347

Total number of rows: 32937

Table truncated, full table size 910 Kbytes.




Supplementary file Size Download File type/resource
GSM272660.txt.gz 350.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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