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SAMPLES (6)

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

Attached file download project data file ('.map')
Attached file (see: ruid website) download project data file ('.map' RUID converted)
Attached file download raw data files ('.zip')
Attached file download annotation files ('.zip')

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

TFIID is a multiprotein complex that plays a pivotal role in the regulation of RNA polymerase II (Pol II) transcription owing to its core promoter recognition and co-activator functions. TAF6 is a core TFIID subunit whose splice variants include the major TAF6delta isoform that is ubiquitously expressed, and the inducible TAF6delta. In contrast to TAF6delta, TAF6delta is a pro-apoptotic isoform with a 10 amino acid deletion in its histone fold domain that abolishes its interaction with TAF9. TAF6delta expression can dictate life versus death decisions of human cells. As a step towards uncovering the molecular basis for the pro-apoptotic activity of TAF6delta, here we define the impact of endogenous TAF6delta expression on the global transcriptome landscape. TAF6delta was found to regulate the expression of genes in the apoptotic pathway, but also genes in the Notch, oxidative stress, integrin, p53, and angiogenesis pathways. Interestingly, gene expression patterns controlled by TAF6delta share similarities with, but are not equivalent to, those reported to change following TAF9 and/or TAF9b depletion. Finally, because TAF6delta regulates certain p53 target genes, we tested and demonstrated a physical and functional interaction between TAF6delta and p53. Together our data define a TAF6delta-driven apoptotic gene expression program and uncover crosstalk between the p53 and TAF6delta pathways.

Technical description

Characteristics 	Hela 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 Î¼g 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 	The Bcl-xS transcription program.
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.

Reference

Wilhelm E, Kornete M, Targat B, Vigneault-Edwards J, Frontini M, Tora L, Benecke A, and Bell B (2009)  TAF6delta orchestrates an apoptotic transcriptome landscape and interacts functionally with p53.

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/20096117