Readme.txt


All ChIP-seq sample data to support the article 

Kim et al (2014) Identification of a novel Bromodomain / Casein Kinase II / TAF-containing complex as a regulator of mitotic condensin function. Cell Reports. doi: 10.1016/j.celrep.2014.01.029

have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO series accession number GSE53955. To visualize the ChIP-seq data we also provide a supporting GenPlay project (GenPlay_Kim_CellRep_2014) which should easily load on most computers. 


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HOW TO DOWNLOAD AND LAUNCH THE PROJECT
1) Download GenPlay from http://genplay.einstein.yu.edu/wiki/index.php/Download and install it by following the instruction specified on this webpage
2) Download the project file at http://genplay.einstein.yu.edu/library/projects/CellReports-2014/Kim_CellRep_2014.gppf
3) Once downloaded, double click on the project file to launch it. The project should load in less than a minute.


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QUICK GenPlay GUIDE:



Once the project is open you are inside the GenPlay Genome analyzer, which was used to process the alignment files (BAM files) and generate most of the data in the article.



Detailed Documentation on the use of GenPlay can be found at:

http://GenPlay.einstein.yu.edu/wiki/index.php/Main_Page  



Below is a short introduction to GenPlay:



Zooming from whole chromosome view to single base pair resolution can be achieved with the mouse wheel or the slider at the bottom of the screen

Navigating to a specific place in the genome can be achieved either by entering coordinates in the box at the lower right  of the screen, or by searching genes by name  after right-clicking on a track containing a layer containing a gene annotation file and accessing the function menu (by hovering over the layer name)  


Most GenPlay functions are accessed through the numbered grey boxes at the left of the screen

Track can be reordered by dragging the numbered grey boxes up or down



Click on the mouse wheel (middle button) to toggle the scroll mode on and off. 

When the scroll mode is on, move the cursor left or right of the middle red line to move within a chromosome.



Left clicking on the grey boxes provides access to the Track Setting menu where scaling and track appearance can be adjusted.

Each track can contain multiple layers. Appearance of each layer can be adjusted by clicking on the layer tab (on the left of the Track setting menu)



Right clicking on the grey boxes provided access to GenPlay Layer modification functions.

From this menu Layers can be added or deleted. They can also be copied or pasted to other Track to create overlays

The names of each loaded Layer are listed at the bottom of the menu. Hovering over the name of the layer opens a menu which allows users to modify the track using a variety of functions.  



Clicking on the tool icon on the upper left of the screen opens a menu which provides access to project saving, help (which brings you to the online documentation) and general GenPlay options.