{"__v":2,"_id":"56e314c46e602e0e00700b35","category":{"__v":17,"_id":"568f0e73bdb9260d00149d8c","pages":["568f0ea29ebef90d0087276a","568f0eafb700ce0d002f4a32","568f0ebbbdb9260d00149d8d","568f0edeb700ce0d002f4a34","568f0ef3bdb9260d00149d8f","568f12099ebef90d0087276d","568f121abeb2700d00471839","568f20e49ebef90d0087277e","568f446d9ebef90d0087278f","56c79a728bf67e0d00734767","56cb8830c675f50b00a4b834","56d47e99a4a9211b00c8f0d2","56d4af6c1c4de4130005d74e","56d52a131c4de4130005d80b","56de001b3db43f2000d9a765","56de1087f25ce60e002e31ad","56e314c46e602e0e00700b35"],"project":"5476bf0f817e8d080031f988","version":"5476bf10817e8d080031f98b","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-01-08T01:18:43.343Z","from_sync":false,"order":1,"slug":"protocols","title":"Premade Protocols"},"parentDoc":null,"project":"5476bf0f817e8d080031f988","user":"54eb9cdbdf7add210007b33e","version":{"__v":17,"_id":"5476bf10817e8d080031f98b","project":"5476bf0f817e8d080031f988","createdAt":"2014-11-27T06:05:04.263Z","releaseDate":"2014-11-27T06:05:04.263Z","categories":["5476bf10817e8d080031f98c","5477c46cf3736008009e9eb5","5477c474f3736008009e9eb6","5477c47ef3736008009e9eb7","5477c48ff3736008009e9eb8","5477c4948deb230800808bf0","54e68328154f8e0d0007b55c","54e90194c8e0c00d007ac061","54eed2275bf74a0d00ef4076","54f7a7be0a3cbb0d00d666fb","559b0ebf7ae7f80d0096d871","55d697f9ae529e0d00d34f03","562d4dcc8c6e5a0d00d6ed1d","562e591c4376430d006f17e0","568f0e73bdb9260d00149d8c","5719542aac1e2e0e001834c6","57a14a8ed778850e0047e230"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-03-11T18:56:04.080Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":6,"body":"[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Description\"\n}\n[/block]\nThis protocol allows you to perform a ligation reaction on at least one fragment of DNA. This protocol uses [Thermo T4 DNA Ligase](https://www.thermofisher.com/order/catalog/product/EL0014). \n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Sample requirements\"\n}\n[/block]\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Sample\",\n    \"h-1\": \"Explanation\",\n    \"0-0\": \"Fragment\",\n    \"0-1\": \"Please select at least one fragment of DNA for your ligation reaction.\",\n    \"1-0\": \"Diluent (from inventory)\",\n    \"1-1\": \"\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Required parameters\"\n}\n[/block]\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Parameter\",\n    \"h-1\": \"Explanation\",\n    \"0-0\": \"Total Reaction Volume\",\n    \"2-0\": \"Fragment volume\",\n    \"3-0\": \"Ligation conditions\",\n    \"4-0\": \"Denaturation conditions\",\n    \"5-0\": \"Storage condition for diluted aliquot\",\n    \"1-0\": \"Ligase volume\",\n    \"0-1\": \"Please specify the total volume for your reaction. This will include the ligase, DNA fragments, buffer, and water. We will automatically determine the amount of buffer and water to add to the reaction based on what you specify for the total reaction volume and the volume of DNA fragments and ligase.\",\n    \"1-1\": \"Please specify the total volume of ligase you would like to use in your reaction. We use [Thermo T4 DNA ligase](https://www.thermofisher.com/order/catalog/product/EL0014) in this reaction.\",\n    \"2-1\": \"Please specify the volume for each DNA fragment you would like to use in your reaction.\",\n    \"3-1\": \"Please specify the incubation conditions for your ligase reaction. [Thermo's control ligation reaction](https://tools.thermofisher.com/content/sfs/manuals/MAN0011965_ControlReaction_T4DNA_Ligase_Activity_UG.pdf) is done at 22C for 10min.\",\n    \"4-1\": \"Please specify denaturations conditions for your ligase reaction. [Thermo](https://www.thermofisher.com/order/catalog/product/EL0014) suggests a denaturation at 70°C for 5 min or 65°C for 10 minutes.\",\n    \"5-1\": \"The storage temperature you require for the diluted sample: either `cold_20`, `cold_4` or `ambient`.\",\n    \"6-0\": \"Diluent\",\n    \"6-1\": \"Select either a diluent from the reagent library or from your inventory.\\n\\nFrom the library both water and TE Buffer are available.\\n\\nFrom your inventory select an aliquot.\"\n  },\n  \"cols\": 2,\n  \"rows\": 5\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Protocol Outputs\"\n}\n[/block]\nThis protocol outputs a new aliquot of the ligated sample which is stored in your inventory at -20°C . Any aliquots used in the making of the sample will be returned to the storage condition from which they came.\n\nNo measurement data is returned by this protocol.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Recommended guidelines\"\n}\n[/block]\nEnsure you are aware of the dead volume in the containers you are using for the fragments. Dead volumes can be found in the containers section [here](https://developers.transcriptic.com/docs/containers#compatible-container-types). Failure to take into account dead volumes can result in insufficient volume being pipetted.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Further reading\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"For further advice on your protocol please ask questions to the community at https://forum.transcriptic.com\",\n  \"title\": \"Check out the forum if you have more questions.\"\n}\n[/block]","excerpt":"","slug":"ligation","type":"basic","title":"Ligation"}
[block:api-header] { "type": "basic", "title": "Description" } [/block] This protocol allows you to perform a ligation reaction on at least one fragment of DNA. This protocol uses [Thermo T4 DNA Ligase](https://www.thermofisher.com/order/catalog/product/EL0014). [block:api-header] { "type": "basic", "title": "Sample requirements" } [/block] [block:parameters] { "data": { "h-0": "Sample", "h-1": "Explanation", "0-0": "Fragment", "0-1": "Please select at least one fragment of DNA for your ligation reaction.", "1-0": "Diluent (from inventory)", "1-1": "" }, "cols": 2, "rows": 1 } [/block] [block:api-header] { "type": "basic", "title": "Required parameters" } [/block] [block:parameters] { "data": { "h-0": "Parameter", "h-1": "Explanation", "0-0": "Total Reaction Volume", "2-0": "Fragment volume", "3-0": "Ligation conditions", "4-0": "Denaturation conditions", "5-0": "Storage condition for diluted aliquot", "1-0": "Ligase volume", "0-1": "Please specify the total volume for your reaction. This will include the ligase, DNA fragments, buffer, and water. We will automatically determine the amount of buffer and water to add to the reaction based on what you specify for the total reaction volume and the volume of DNA fragments and ligase.", "1-1": "Please specify the total volume of ligase you would like to use in your reaction. We use [Thermo T4 DNA ligase](https://www.thermofisher.com/order/catalog/product/EL0014) in this reaction.", "2-1": "Please specify the volume for each DNA fragment you would like to use in your reaction.", "3-1": "Please specify the incubation conditions for your ligase reaction. [Thermo's control ligation reaction](https://tools.thermofisher.com/content/sfs/manuals/MAN0011965_ControlReaction_T4DNA_Ligase_Activity_UG.pdf) is done at 22C for 10min.", "4-1": "Please specify denaturations conditions for your ligase reaction. [Thermo](https://www.thermofisher.com/order/catalog/product/EL0014) suggests a denaturation at 70°C for 5 min or 65°C for 10 minutes.", "5-1": "The storage temperature you require for the diluted sample: either `cold_20`, `cold_4` or `ambient`.", "6-0": "Diluent", "6-1": "Select either a diluent from the reagent library or from your inventory.\n\nFrom the library both water and TE Buffer are available.\n\nFrom your inventory select an aliquot." }, "cols": 2, "rows": 5 } [/block] [block:api-header] { "type": "basic", "title": "Protocol Outputs" } [/block] This protocol outputs a new aliquot of the ligated sample which is stored in your inventory at -20°C . Any aliquots used in the making of the sample will be returned to the storage condition from which they came. No measurement data is returned by this protocol. [block:api-header] { "type": "basic", "title": "Recommended guidelines" } [/block] Ensure you are aware of the dead volume in the containers you are using for the fragments. Dead volumes can be found in the containers section [here](https://developers.transcriptic.com/docs/containers#compatible-container-types). Failure to take into account dead volumes can result in insufficient volume being pipetted. [block:api-header] { "type": "basic", "title": "Further reading" } [/block] [block:callout] { "type": "success", "body": "For further advice on your protocol please ask questions to the community at https://forum.transcriptic.com", "title": "Check out the forum if you have more questions." } [/block]