{"__v":5,"_id":"572a85db54312934004c757f","category":{"__v":19,"_id":"54f7a7be0a3cbb0d00d666fb","pages":["54f7a95354182d2100c9d057","54f7ad293607243500de2496","54f7ae7d0a3cbb0d00d66705","54f7b0013607243500de249b","54f7b4360a3cbb0d00d6670c","54f7c71154182d2100c9d073","54fa5205961fea21009206a9","54fa55e1c6db4517005b0147","54fddf642804410d00ee8a2a","5509fd2bdfed731900b81863","552dfa862594f70d001b2c48","552dfab3a702770d00d96d5b","552dfaca2594f70d001b2c4a","55d68d2c250d7d0d00427478","55d68d3bae529e0d00d34edb","5611dd433ca69417008981af","5679bca976cd370d003c1183","56de30df9ca83e17000cbc59","56eadf62199f7317006eb4db"],"project":"5476bf0f817e8d080031f988","version":"5476bf10817e8d080031f98b","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-03-05T00:47:58.582Z","from_sync":false,"order":4,"slug":"instructions","title":"Capabilities"},"parentDoc":null,"project":"5476bf0f817e8d080031f988","user":"56f57b8eab3f610e000a6596","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":"2016-05-04T23:29:31.926Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":true,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":7,"body":"[block:callout]\n{\n  \"type\": \"danger\",\n  \"title\": \"Beta\",\n  \"body\": \"The `gel_purify` instruction is currently in beta and may change as capabilities develop.\"\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Instruction and Parameters\"\n}\n[/block]\n\n[block:textarea]\n{\n  \"text\": \"##Gel Separate\\n`gel_separate` takes an aliquot and runs it on a agarose gel, an image of which will be viewable in the \\\"results\\\" tab within the run. The physical aliquot is destroyed.\",\n  \"sidebar\": true\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"danger\",\n  \"title\": \"Gel Quantitation\",\n  \"body\": \"We do not recommend using this instruction for DNA quantitation. Instead, please see the [Picogreen Assay](doc:picogreen-assay) protocol.\"\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"gel_separate\\\",\\n  \\\"volume\\\": volume,\\n  \\\"objects\\\": [wells],\\n  \\\"matrix\\\": \\\"agarose(10,2%)\\\" | \\\"agarose(10,1.2%)\\\" | \\\"agarose(10,0.8%)\\\" | \\\"agarose(48,2%)\\\" | \\\"size_select(8,2%)\\\",\\n  \\\"ladder\\\": \\\"ladder1\\\" | \\\"ladder2\\\",\\n  \\\"duration\\\": duration,\\n  \\\"dataref\\\": string\\n}\",\n      \"language\": \"json\",\n      \"name\": \"gel_separate\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\nWe run a dry gel format that has two major differences compared to standard gel electrophoresis: the voltage is fixed and the durations are generally much shorter. `agarose` gels cannot be run for more than 30 minutes.\n\nThe available gels and their recommended run times are:\n[block:html]\n{\n  \"html\": \"<style>dd {\\n    margin-bottom: 10px;\\n  }\\n  dl {\\n    padding-left: 10px;\\n    border-left: 3px solid #eee;\\n    dt code {\\n      font-weight: normal;\\n    }\\n  }\\n</style>\\n<dl>\\n  <dt><code>agarose(10,0.8%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 10 minutes. Uses ethidium bromide. Ladder (12 uL) is loaded on both edges of the gel.</dd>\\n  <dt><code>agarose(10,1.2%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 10 minutes. Uses SYBR green. Ladder (12 uL) is loaded on both edges of the gel.</dd>\\n  <dt><code>agarose(10,2%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 15 minutes. Uses SYBR green. Ladder (12 uL) is loaded on both edges of the gel.</dd>\\n  <dt><code>agarose(48,2%)</code></dt> <dd>48 wells. 15 uL sample volume per well. Suggested run time 15 minutes. Uses ethidium bromide. Ladder (12 uL) is loaded on both edges of the gel.</dd> \\n</dl>\"\n}\n[/block]\nThe specified ladder will be run in an additional center lane on each gel. You should pick a ladder which corresponds to the size of product you're expecting. Although the volume of ladder used is listed above, use of `gel_separate` is not recommended for DNA quantitation.\n\n`ladder1`\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/dz1WTKfBROuk9F0fltRL_ladder1-BiolineEasyLadderI.png\",\n        \"ladder1-BiolineEasyLadderI.png\",\n        \"225\",\n        \"330\",\n        \"#cdcdcd\",\n        \"\"\n      ],\n      \"caption\": \"ladder1\"\n    }\n  ]\n}\n[/block]\n `ladder2`\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/lPM3ecG4RpWiE4rgRKka_ladder2-ThermoFastRulerHR.png\",\n        \"ladder2-ThermoFastRulerHR.png\",\n        \"358\",\n        \"175\",\n        \"#353535\",\n        \"\"\n      ],\n      \"caption\": \"ladder2\",\n      \"sizing\": \"smart\"\n    }\n  ]\n}\n[/block]\n`ladder1` corresponds to the Bioline EasyLadder I. More information can be found [here](http://www.bioline.com/us/easyladder-i.html).\n\n`ladder2` corresponds to the ThermoFisher FastRuler High Range DNA Ladder. More information can be found [here](https://www.thermofisher.com/order/catalog/product/SM1123).\n\n##Gel Purify\n`gel_purify` is similar to `gel_separate` in that it takes an aliquot with `volume` less than or equal to 25:microliter and runs it on an agarose gel, but with the addition of an `extract` array. `extract` is an array of extraction groups, which may each have different parameters, specifying the target DNA and other details for band extraction.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"gel_purify\\\",\\n  \\\"volume\\\": volume,\\n  \\\"objects\\\": [wells],\\n  \\\"matrix\\\": \\\"size_select(8,2%)\\\",\\n  \\\"ladder\\\": ladder,\\n  \\\"dataref\\\": string,\\n  \\\"extract\\\": [{\\n    \\\"elution_volume\\\": \\\"25:microliter\\\",\\n    \\\"elution_buffer\\\": \\\"water\\\",\\n    \\\"lane\\\": int,\\n    \\\"band_size_range\\\": {\\n      \\\"min_bp\\\": int,\\n      \\\"max_bp\\\": int,\\n    },\\n    \\\"destination\\\": well\\n  }, \\n  {...}]\\n}\",\n      \"language\": \"json\",\n      \"name\": \"gel_purify\"\n    }\n  ]\n}\n[/block]\n`elution_volume` is the final volume that a solution of extracted DNA should be returned in, and must be equal to \"25:microliter\". `elution_buffer` is the solution that the DNA should be returned in, for which `\"water\"` is currently the only option. After the instruction is completed, the `dataref` will be associated with an image of the gel with boxes around the bands that were purified, indicating the approximate purified area of the gel.\n\nIn the `extract` array, `lane` indicates the gel lane from which DNA should be `extract`ed. The `band_size_range` parameters indicate the base pair size range of the band to be extracted, which must be between 50 and 10,000 base pairs. Finally, each `extract` group takes a `destination` well where the extracted DNA in the elution buffer should be deposited.\n\nFor `ladder` options, please see the `gel_separate` information above.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Band Size Range\",\n  \"body\": \"The difference between `min_bp` and `max_bp` for each extract must be between 50 and 500 base pairs. The current implementation of `gel_purify` is inexact. We will try to harvest all bands present in the band size range given.\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Gel Purification Capacity\",\n  \"body\": \"The `size_select` gels used in the gel purification instruction have a maximum theoretical capacity of 700ng/lane and a detection limit of 1.5ng/band. These are theoretical limits and we strongly recommend not overloading or underloading the gel as this can impact the efficiency of purification.\"\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Device\"\n}\n[/block]\nThe `gel_separate` instruction uses Lifetech's E-Gel system, and the `gel_purify` instruction uses Lifetech's E-Gel SizeSelect system. Gels cannot be reused. A ladder is always run with the samples and is located in either the center of the gel or on both edges depending on gel type (see chart above). \n\nMore details on E-Gels and their recommended run times can be found [here](https://tools.lifetechnologies.com/content/sfs/manuals/egelguide_man.pdf).\n\nMore details on the E-Gel SizeSelect system can be found [here](https://www.thermofisher.com/order/catalog/product/G661002).\n\nImaging on the Bio-Rad EZ Gel Imager is handled implicitly for `gel_separate` and `gel_purify`.","excerpt":"","slug":"gel-electrophoresis","type":"basic","title":"Gel Electrophoresis"}

Gel Electrophoresis


[block:callout] { "type": "danger", "title": "Beta", "body": "The `gel_purify` instruction is currently in beta and may change as capabilities develop." } [/block] [block:api-header] { "type": "basic", "title": "Instruction and Parameters" } [/block] [block:textarea] { "text": "##Gel Separate\n`gel_separate` takes an aliquot and runs it on a agarose gel, an image of which will be viewable in the \"results\" tab within the run. The physical aliquot is destroyed.", "sidebar": true } [/block] [block:callout] { "type": "danger", "title": "Gel Quantitation", "body": "We do not recommend using this instruction for DNA quantitation. Instead, please see the [Picogreen Assay](doc:picogreen-assay) protocol." } [/block] [block:code] { "codes": [ { "code": "{\n \"op\": \"gel_separate\",\n \"volume\": volume,\n \"objects\": [wells],\n \"matrix\": \"agarose(10,2%)\" | \"agarose(10,1.2%)\" | \"agarose(10,0.8%)\" | \"agarose(48,2%)\" | \"size_select(8,2%)\",\n \"ladder\": \"ladder1\" | \"ladder2\",\n \"duration\": duration,\n \"dataref\": string\n}", "language": "json", "name": "gel_separate" } ], "sidebar": true } [/block] We run a dry gel format that has two major differences compared to standard gel electrophoresis: the voltage is fixed and the durations are generally much shorter. `agarose` gels cannot be run for more than 30 minutes. The available gels and their recommended run times are: [block:html] { "html": "<style>dd {\n margin-bottom: 10px;\n }\n dl {\n padding-left: 10px;\n border-left: 3px solid #eee;\n dt code {\n font-weight: normal;\n }\n }\n</style>\n<dl>\n <dt><code>agarose(10,0.8%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 10 minutes. Uses ethidium bromide. Ladder (12 uL) is loaded on both edges of the gel.</dd>\n <dt><code>agarose(10,1.2%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 10 minutes. Uses SYBR green. Ladder (12 uL) is loaded on both edges of the gel.</dd>\n <dt><code>agarose(10,2%)</code></dt> <dd>10 wells. 20 uL sample volume per well. Suggested run time 15 minutes. Uses SYBR green. Ladder (12 uL) is loaded on both edges of the gel.</dd>\n <dt><code>agarose(48,2%)</code></dt> <dd>48 wells. 15 uL sample volume per well. Suggested run time 15 minutes. Uses ethidium bromide. Ladder (12 uL) is loaded on both edges of the gel.</dd> \n</dl>" } [/block] The specified ladder will be run in an additional center lane on each gel. You should pick a ladder which corresponds to the size of product you're expecting. Although the volume of ladder used is listed above, use of `gel_separate` is not recommended for DNA quantitation. `ladder1` [block:image] { "images": [ { "image": [ "https://files.readme.io/dz1WTKfBROuk9F0fltRL_ladder1-BiolineEasyLadderI.png", "ladder1-BiolineEasyLadderI.png", "225", "330", "#cdcdcd", "" ], "caption": "ladder1" } ] } [/block] `ladder2` [block:image] { "images": [ { "image": [ "https://files.readme.io/lPM3ecG4RpWiE4rgRKka_ladder2-ThermoFastRulerHR.png", "ladder2-ThermoFastRulerHR.png", "358", "175", "#353535", "" ], "caption": "ladder2", "sizing": "smart" } ] } [/block] `ladder1` corresponds to the Bioline EasyLadder I. More information can be found [here](http://www.bioline.com/us/easyladder-i.html). `ladder2` corresponds to the ThermoFisher FastRuler High Range DNA Ladder. More information can be found [here](https://www.thermofisher.com/order/catalog/product/SM1123). ##Gel Purify `gel_purify` is similar to `gel_separate` in that it takes an aliquot with `volume` less than or equal to 25:microliter and runs it on an agarose gel, but with the addition of an `extract` array. `extract` is an array of extraction groups, which may each have different parameters, specifying the target DNA and other details for band extraction. [block:code] { "codes": [ { "code": "{\n \"op\": \"gel_purify\",\n \"volume\": volume,\n \"objects\": [wells],\n \"matrix\": \"size_select(8,2%)\",\n \"ladder\": ladder,\n \"dataref\": string,\n \"extract\": [{\n \"elution_volume\": \"25:microliter\",\n \"elution_buffer\": \"water\",\n \"lane\": int,\n \"band_size_range\": {\n \"min_bp\": int,\n \"max_bp\": int,\n },\n \"destination\": well\n }, \n {...}]\n}", "language": "json", "name": "gel_purify" } ] } [/block] `elution_volume` is the final volume that a solution of extracted DNA should be returned in, and must be equal to "25:microliter". `elution_buffer` is the solution that the DNA should be returned in, for which `"water"` is currently the only option. After the instruction is completed, the `dataref` will be associated with an image of the gel with boxes around the bands that were purified, indicating the approximate purified area of the gel. In the `extract` array, `lane` indicates the gel lane from which DNA should be `extract`ed. The `band_size_range` parameters indicate the base pair size range of the band to be extracted, which must be between 50 and 10,000 base pairs. Finally, each `extract` group takes a `destination` well where the extracted DNA in the elution buffer should be deposited. For `ladder` options, please see the `gel_separate` information above. [block:callout] { "type": "warning", "title": "Band Size Range", "body": "The difference between `min_bp` and `max_bp` for each extract must be between 50 and 500 base pairs. The current implementation of `gel_purify` is inexact. We will try to harvest all bands present in the band size range given." } [/block] [block:callout] { "type": "warning", "title": "Gel Purification Capacity", "body": "The `size_select` gels used in the gel purification instruction have a maximum theoretical capacity of 700ng/lane and a detection limit of 1.5ng/band. These are theoretical limits and we strongly recommend not overloading or underloading the gel as this can impact the efficiency of purification." } [/block] [block:api-header] { "type": "basic", "title": "Device" } [/block] The `gel_separate` instruction uses Lifetech's E-Gel system, and the `gel_purify` instruction uses Lifetech's E-Gel SizeSelect system. Gels cannot be reused. A ladder is always run with the samples and is located in either the center of the gel or on both edges depending on gel type (see chart above). More details on E-Gels and their recommended run times can be found [here](https://tools.lifetechnologies.com/content/sfs/manuals/egelguide_man.pdf). More details on the E-Gel SizeSelect system can be found [here](https://www.thermofisher.com/order/catalog/product/G661002). Imaging on the Bio-Rad EZ Gel Imager is handled implicitly for `gel_separate` and `gel_purify`.