Brachyury_ChIP_sequencing_of_human_chordoma_UCH_1_cell_line-sc-2011-10-17T14:30:38Z-341
Brachyury_ChIP_sequencing_of_human_chordoma_UCH_1_cell_line
A well characterised chordoma cell line which bears all the morphological and immunohistochemical features of a chordoma (large vacuolated slow-growing cells, brachyury and cytokeratin-positive) will be used in this study. Chromatin immunoprecipitation using a well characterised anti-Brachyury antibody which has been used in immunohistochemistry of chordoma samples and previous ChIP studies in other systems.For each sample 1x106 cells were collected and subjected to immunoprecipitation with anti-Brachyury antibody as described in Morley et al, 2009, PNAS 106(10):3829-34. ChIPed DNA was amplified using PE adapters from Illumina and this library was size selected then sequenced on the Illumina GAII platform.  This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
ChIP sequencing of chordoma UCH-1 cell line  AIM: the aim of this project is to identify transcriptional targets of brachyury in a human chordoma cell line   Background:  Chordomas are rare bone tumours arising in the base of skull and vertebral bodies with less than 100 presenting the in the UK per annum.  The average length of survival from presentation is 7 years and up to 40% of tumours metastasise. There are almost no genetic events known to occur in this tumour and the absence of this information hampers the development of directed therapies.    Chordomas show notochordal differentiation with brachyury being the molecular signature of this tumour.  Brachyury, a transcription factor, is crucial in the development of the mesoderm but little is known about its transcriptional targets particularly in humans.    Potential benefit of the study: Knowledge of brachyury transcriptional targets would potentially reveal new opportunities to identify therapeutic targets for this tumour. The study would also provide elucidate the molecular events in the development of the notochord in health and disease.  Materials & Methods A well characterised chordoma cell line which bears all the morphological and immunohistochemical features of a chordoma (large vacuolated slow-growing cells, brachyury and cytokeratin-positive) will be used in this study. Chromatin immunoprecipitation using a well characterised anti-Brachyury antibody which has been used in immunohistochemistry of chordoma samples and previous ChIP studies in other systems. Preliminary data: Data from preliminary ChIP-PCR experiments indicates that Brachyury binds genomic regions around  DDR1 and PPL - two genes whose expression is up-regulated in chordoma tissue.