I would check which/where exactly the files are that take up all the space. You can do this through the cli (as InKo pointed out) or using the nice graphical tool that comes with gnome, the disk-usage analyzer. Go to Applications, System-tools, Disk-usage analyzer (translated from German, might have a slightly different name on your system). Click the "read filesystem" button and voilą, everything is listed and has additionally a nice graphical display on the right side to examine more about the disk-usage.
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