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What are Rune Bottles? Rune bottles can be found throughout certain dungeons, and you can get them from killing (and or) stealing from Chimaeras on the Fooji Mtns, Undertakers in Gaoracchia Forest, Storm Claws in Ymir Forest, the big snake "Silver" in the Flanoir area, and other enemies that I'm just too lazy to list. But if you kill easier enemies, you can get a higher GP, and have a easier time obtaining items. Well now to answer my question.
   Rune Bottles can be found in your "Gel Section" of your inventory. They are used to transform normal items in your inventory, to more powerful versions, or alternate versions of the original item. For example, an Apple Gel will turn into a more "powerful" form; a Lemon Gel. While Energy Tablets will turn into their "alternate" form; Spirit Bottles, which recovers Tp as opposed to Hp.
   So you may be thinking, is it really worth it? Yes it is. Even though you still can find the "transformed" items, its much more useful early in the game. You can change Sages (which raises max Hp by 5%) to Red Sages (which raises max Hp by 10%), obviously a better choice. After such a lengthy explanation of what Rune bottles do, this is how to use them. Just go in your inventory, and click the Rune Bottle, and it will bring you to a seperate little menu with items that you are able to transform (Don't go looking for possible weapon transformations, as far as I know, you cannot do it).


Status Items
Original Transformed New Effects Type
Apple Gel Lemon Gel Recover 60% Hp Any
Orange Gel Pineapple Gel Recover 60% Tp Any
Melange Gel Miracle Gel Recover 60% Hp & Tp Any
Energy Tablets Spirit Bottle Recover 30% Tp all Any
Panacea Bottle Miracle Bottle Cures all status (except KO) Any
Acuity Bottle Guard Bottle Defense up 10% Battle
Flare Bottle Acuity Bottle Accuracy up 10% Battle
Guard Bottle Flare Bottle Attack up 10% Battle
Shell Bottle Syrup Bottle Protects against physical status & attack down by 20% Battle
Syrup Bottle Shell Bottle Protects against magical status & attack down by 20% Battle


Herbs
Original Transformed New Effects Type
Bellbane Red Bellbane Raise Max Def by 3 Non-Battle
Lavender Red Lavender Raise Max Str by 3 Non-Battle
Saffron Red Saffron Raise Max Eva by 3 Non-Battle
Rosemary Red Rosemary Raise Max Acc by 3 Non-Battle
Savory Red Savory Raise Max Tp by 10% Non-Battle
Sage Red Sage Raise Max Hp by 10% Non-Battle


Quartz
Original Transformed New Effects Type
Aqua Quartz Purple Quartz Adds Lightning element to attacks Battle
Blue Quartz Red Quartz Adds Fire element to attacks Battle
Green Quartz Yellow Quartz Adds Earth element to attacks Battle
Purple Quartz Aqua Quartz Adds Water element to attacks Battle
Red Quartz Blue Quartz Adds Ice element to attacks Battle
Yellow Quartz Green Quartz Adds Wind element to attacks Battle


Accesories
Original Transformed New Effects Type
Holy Ring Spirit Ring Recovers 1% Hp during fights Equipment
Spirit Ring Holy Ring Recovers 1% Tp during fights Equipment
Spirit Symbol Holy Symbol Recovers 3% Hp during fights Equipment
Holy Symbol Spirit Symbol Recovers 3% Tp during fights Equipment
Blue Talisman Talisman Raises Def by 5% Equipment
Warrior Symbol Guardian Symbol Raises Def by 10% Equipment
Talisman Blue Talisman Raises Def by 15% Equipment
Guardian Symbol Warrior Symbol Raises Str by 10% Equipment
Protect Ring Resist Ring Reduce magic damage but raise physical damage Equipment
Resist Ring Protect Ring Reduce physical damage but raise magic damage Equipment
Spirit Bangle Heal Bracelet Recover 10% Hp on kill Equipment
Heal Bracelet Spirit Bangle Recover 5% Tp on kill Equipment
Reverse Doll Sephira Receive 50% more gald after fights Equipment
Sephira Blue Sephira Receive 100% more gald after fights Equipment
Blue Sephira Reverse Doll Automatically Revive after death Equipment


Confused on how to read the table? Well the first column, Original, is the Original Item that you are wishing to transform. The second column, Transformed is the new item that the original one changed into. Then the third column, New Effects is the new effect of the item that was changed (not the original item's effects). And finally the fourth column, Type is when you can use your newly made items. The types are;
Any: These items can be used at anytime you wish. These are normally healing items like Gels or Life Bottles
Battle: Simply put, useable only in battle, and the effects will wear off when the fight is done.
Non-Battle: You can not use these items in battle, and can only be used when you are wandering the world map, or towns.
Equipment: Are accesories that can be equipped during battle, as well as out of battle.


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