2019 Year 12 IB Extended Essays

2 Method and Procedure

The process of determining selecting the vital transcription factors involve: - Obtaining the active transcription factors present in the cell - For each transcription factor, the specificity of expression to the target cell type is examined (it may be a single factor or a unique combination of factors) - For each transcription factor, examine possible undesirable effects associated with the transcription factors 2.1 Obtaining the active transcription factors in iCPCs Researchers from the study mentioned in section 1.2 (Ieda, et al., 2010) selected 14 of the early cardiac factors as the starting material and narrowed down to the three most significant transcription factors involved in the transformation process. In this investigation, an elimination process will be conducted to obtain the most suitable and exclusive transcription factors out of the 14. The transcription factors are: Baf60c, Gata4, Hand2, Hopx, Hrt2, Isl1, Mef2c, Mesp1, Myacd, Nkx2.5, Pitx2c, Smyd1, Srf, Tbx5. 2.2 Examining the specificity of each transcription factor After obtaining the list of active transcription factors in iCPCs, the next step is to examine the specificity of the transcription factors to this cell type. Researchers will need to look at the tissue microarray, which is a tool enabling researchers to look at a certain group of cells or tissue and see what genes are being expressed. Some transcription factors are also highly expressed in other cells and thus will be concluded not specific. However, if a unique combination of transcription factors has been discovered exclusive to iCPCs, then this can be considered specific. Amazonia! , a microarray database is needed for this examination. 1. Create a table with headings as follows: Target cell type Important transcription factors Other cell types that expresses it Highly expressed In other cell types? Known functions 2. Access the Amazonia! Microarray database at: http://amazonia.transcriptome.eu and search for the first transcription factor of the table (Baf60c) press ‘Go!’. 3. Click on the top graph displayed in the screen to expand it. On the x-axis there are cell types listed. For each cell type the level of gene expression for this particular gene is shown on the y-axis.

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