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SAMPLES (12)

mace:id
Technology # Array version
Species
Organ
Tissue
Physiopathology
Type
Name

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User name	Arndt Benecke
Email	arndt@ihes.fr
Phone / Fax number	+33160926665 / +33160926609
Location	Institut des Hautes Etudes Scientifiques (Integrative Biology) - 35, route de Chartres - 91440 Bures sur Yvette, France

Scientific description

To elucidate the impact of TAF6d on cell death and gene expression, here we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6d. The induction of endogenous TAF6d triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6d activates gene expression independently of cellular p53 status. Our data define TAF6d as a pivotal node in a signaling pathway that acts immediately downstream of p53 to control gene expression programmes and apoptosis.
Keywords: Treatment with splice site switching antisense oligonucleotides, induction of apoptosis
Colorectal carcinoma male cell line

Technical description

Characteristics 	HCT-116 p53-/- cells + Control antisense 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 Âµg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturerâ€™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 manufacturerâ€™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 manufacturerâ€™s protocol (P/N 4339629).
Description 	ctrl AS 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.

References

Wilhelm E, Pellay FX, Benecke A, Bell B (2008) TAF6delta controls apoptosis and gene expression in the absence of p53. PLoS One. 3(7): e2721.

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/18628956

previously published on GEO as dataset: GSE10795