{"_id":"54f7ad293607243500de2496","user":"54e3d35e464a9c3700f7ca7f","__v":18,"parentDoc":null,"project":"5476bf0f817e8d080031f988","category":{"_id":"54f7a7be0a3cbb0d00d666fb","version":"5476bf10817e8d080031f98b","__v":19,"project":"5476bf0f817e8d080031f988","pages":["54f7a95354182d2100c9d057","54f7ad293607243500de2496","54f7ae7d0a3cbb0d00d66705","54f7b0013607243500de249b","54f7b4360a3cbb0d00d6670c","54f7c71154182d2100c9d073","54fa5205961fea21009206a9","54fa55e1c6db4517005b0147","54fddf642804410d00ee8a2a","5509fd2bdfed731900b81863","552dfa862594f70d001b2c48","552dfab3a702770d00d96d5b","552dfaca2594f70d001b2c4a","55d68d2c250d7d0d00427478","55d68d3bae529e0d00d34edb","5611dd433ca69417008981af","5679bca976cd370d003c1183","56de30df9ca83e17000cbc59","56eadf62199f7317006eb4db"],"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-03-05T00:47:58.582Z","from_sync":false,"order":4,"slug":"instructions","title":"Capabilities"},"version":{"_id":"5476bf10817e8d080031f98b","__v":17,"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":"2015-03-05T01:11:05.344Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":22,"body":"[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Instruction and Parameters\"\n}\n[/block]\nA `thermocycle` step can either be at a constant temperature or with a gradient applied row-wise down the plate. Constant temperatures can range from 0°C - 100°C, and gradient temperatures can range from 30°C - 100°C. Additionally, the difference between the `top` and `bottom` temperatures in a gradient step must range from 1°C - 24°C, with the `top` parameter being the greater temperature. Temperatures and durations can be changed in increments of 0.1°C and 1 second, respectively.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"thermocycle\\\",\\n  \\\"object\\\": container,\\n  \\\"volume\\\": volume,\\n  \\\"groups\\\": [{\\n    \\\"cycles\\\": integer,\\n    \\\"steps\\\": [{\\n      \\\"duration\\\": duration,\\n      \\\"temperature\\\": temperature,\\n      \\\"read\\\": boolean // optional (default false)\\n    },{\\n      \\\"duration\\\": duration,\\n      \\\"gradient\\\": {\\n        \\\"top\\\": temperature,\\n        \\\"bottom\\\": temperature\\n      },\\n      \\\"read\\\": boolean // optional (default false)\\n    }]\\n  }],\\n\\n  // optionally\\n  \\\"dyes\\\": {\\n    <dye_name>: [well]\\n  },\\n  \\\"dataref\\\": string,\\n  \\\"melting\\\": {\\n    \\\"start\\\": temperature,\\n    \\\"end\\\": temperature,\\n    \\\"increment\\\": temperature,\\n    \\\"rate\\\": duration\\n  }\",\n      \"language\": \"json\",\n      \"name\": \"thermocycle\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Plate type\",\n    \"h-1\": \"Maximum volume\",\n    \"0-1\": \"50uL\",\n    \"1-1\": \"30uL\",\n    \"0-0\": \"`96-pcr`\",\n    \"1-0\": \"`384-pcr`\"\n  },\n  \"cols\": 2,\n  \"rows\": 2\n}\n[/block]\n\nThe `dyes` object is a map from a selected fluorophore to the list of wells that contain it. Both the `dyes` and `dataref` objects are not specified in a regular `thermocycle` instruction, but must be specified if any real-time measurements are to be specified. Any of the `steps` of a thermocycle `group` may enable an optional boolean read parameter to signal a qPCR reading after its corresponding step. The default value for `read` is `false`.\n\n  For real-time measurements, the available `dyes` 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>Channel 1</dt> <dd>\\n  Excitation range: 450nm - 490nm <br>\\n  Emission range: 510nm - 530nm <br>\\n  Detectable dyes: <code>FAM</code>,<code>SYBR</code>\\n  </dd>\\n  <dt>Channel 2</dt> <dd>\\n  Excitation range: 515nm - 535nm <br>\\n  Emission range: 560nm - 580nm <br>\\n  Detectable dyes: <code>VIC</code>,<code>HEX</code>,<code>TET</code>,<code>CALGOLD540</code>\\n  </dd> \\n  <dt>Channel 3</dt> <dd>\\n  Excitation range: 560nm - 590nm <br>\\n  Emission range: 675nm - 690nm <br>\\n  Detectable dyes: <code>ROX</code>,<code>TXR</code>,<code>QUASAR670</code>\\n  </dd>\\n  <dt>Channel 4</dt> <dd>\\n  Excitation range: 620nm - 650nm <br>\\n  Emission range: 675nm - 690nm <br>\\n  Detectable dyes: <code>CY5</code>,<code>QUASAR670</code>\\n  </dd>\\n  <dt>Channel 5</dt> <dd>\\n  96-well plates only <br>\\n  Excitation range: 672nm - 684nm <br>\\n  Emission range: 705nm - 730nm <br>\\n  Detectable dyes:<code>QUASAR705</code>\\n  </dd>\\n</dl>\"\n}\n[/block]\nAn optional `melting` object may be included at the end of the thermocycle instruction. It will take its `dye` configuration from the top-level dyes object. Its temperature `increment` parameter may take values from 0.1°C - 9.9°C. Note that a melt has an implicit 30 second hold at its beginning.\n\nThe `volume` parameter denotes the sample volume, which is used to estimate the sample temperature. This helps to maintain consistency between the intended and actual behavior of thermocycle instructions. The value of volume must be between 0uL - 50uL for 96 well plates and 0uL - 30uL for 384 well plates, and it will be rounded to the nearest microliter.\n\nPlates must be sealed using the `seal` instruction before any thermocycler instructions can be executed. Submitting a protocol that thermocycles an unsealed plate will yield an error message.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Device\"\n}\n[/block]\nAll `thermocycle` instructions will be executed on a Bio-Rad CFX96 or CFX384 system depending on the plate type used. The per minute costs are tiered, depending on your use of the quantitation system.\n\n## Standard Operation\nThe average ramp rate of the CFX thermocyclers is 3.3°C with a maximum of 5°C. Gradients can be run from 30°C to 100°C with a total temperature span between 1°C and 24°C. The temperature accuracy has been determined to be ±0.2°C of the target temperature with a well-to-well uniformity of ±0.4°C within 10 seconds of arriving at the target temperature.\n\n## Optics\nThe optics use 6 filtered LEDs and photodiodes. Using LEDs provides some major advantages over lamp-based systems. Lamp-based systems are passive and as such the light path lengths is different for every well. A well with a shorter light path will have a higher fluorescence reading compared to a well with a longer path. To compensate for this effect the data has to be normalized by a reference dye. The LED based system does not require that, as the LEDs are positioned directly over each well - resulting in equal length light path. More details on the devices can be found on the [Bio-Rad website](http://www.bio-rad.com/en-us/product/cfx96-touch-real-time-pcr-detection-system).","excerpt":"","slug":"thermocycling","type":"basic","title":"Thermocycling"}
[block:api-header] { "type": "basic", "title": "Instruction and Parameters" } [/block] A `thermocycle` step can either be at a constant temperature or with a gradient applied row-wise down the plate. Constant temperatures can range from 0°C - 100°C, and gradient temperatures can range from 30°C - 100°C. Additionally, the difference between the `top` and `bottom` temperatures in a gradient step must range from 1°C - 24°C, with the `top` parameter being the greater temperature. Temperatures and durations can be changed in increments of 0.1°C and 1 second, respectively. [block:code] { "codes": [ { "code": "{\n \"op\": \"thermocycle\",\n \"object\": container,\n \"volume\": volume,\n \"groups\": [{\n \"cycles\": integer,\n \"steps\": [{\n \"duration\": duration,\n \"temperature\": temperature,\n \"read\": boolean // optional (default false)\n },{\n \"duration\": duration,\n \"gradient\": {\n \"top\": temperature,\n \"bottom\": temperature\n },\n \"read\": boolean // optional (default false)\n }]\n }],\n\n // optionally\n \"dyes\": {\n <dye_name>: [well]\n },\n \"dataref\": string,\n \"melting\": {\n \"start\": temperature,\n \"end\": temperature,\n \"increment\": temperature,\n \"rate\": duration\n }", "language": "json", "name": "thermocycle" } ], "sidebar": true } [/block] [block:parameters] { "data": { "h-0": "Plate type", "h-1": "Maximum volume", "0-1": "50uL", "1-1": "30uL", "0-0": "`96-pcr`", "1-0": "`384-pcr`" }, "cols": 2, "rows": 2 } [/block] The `dyes` object is a map from a selected fluorophore to the list of wells that contain it. Both the `dyes` and `dataref` objects are not specified in a regular `thermocycle` instruction, but must be specified if any real-time measurements are to be specified. Any of the `steps` of a thermocycle `group` may enable an optional boolean read parameter to signal a qPCR reading after its corresponding step. The default value for `read` is `false`. For real-time measurements, the available `dyes` 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>Channel 1</dt> <dd>\n Excitation range: 450nm - 490nm <br>\n Emission range: 510nm - 530nm <br>\n Detectable dyes: <code>FAM</code>,<code>SYBR</code>\n </dd>\n <dt>Channel 2</dt> <dd>\n Excitation range: 515nm - 535nm <br>\n Emission range: 560nm - 580nm <br>\n Detectable dyes: <code>VIC</code>,<code>HEX</code>,<code>TET</code>,<code>CALGOLD540</code>\n </dd> \n <dt>Channel 3</dt> <dd>\n Excitation range: 560nm - 590nm <br>\n Emission range: 675nm - 690nm <br>\n Detectable dyes: <code>ROX</code>,<code>TXR</code>,<code>QUASAR670</code>\n </dd>\n <dt>Channel 4</dt> <dd>\n Excitation range: 620nm - 650nm <br>\n Emission range: 675nm - 690nm <br>\n Detectable dyes: <code>CY5</code>,<code>QUASAR670</code>\n </dd>\n <dt>Channel 5</dt> <dd>\n 96-well plates only <br>\n Excitation range: 672nm - 684nm <br>\n Emission range: 705nm - 730nm <br>\n Detectable dyes:<code>QUASAR705</code>\n </dd>\n</dl>" } [/block] An optional `melting` object may be included at the end of the thermocycle instruction. It will take its `dye` configuration from the top-level dyes object. Its temperature `increment` parameter may take values from 0.1°C - 9.9°C. Note that a melt has an implicit 30 second hold at its beginning. The `volume` parameter denotes the sample volume, which is used to estimate the sample temperature. This helps to maintain consistency between the intended and actual behavior of thermocycle instructions. The value of volume must be between 0uL - 50uL for 96 well plates and 0uL - 30uL for 384 well plates, and it will be rounded to the nearest microliter. Plates must be sealed using the `seal` instruction before any thermocycler instructions can be executed. Submitting a protocol that thermocycles an unsealed plate will yield an error message. [block:api-header] { "type": "basic", "title": "Device" } [/block] All `thermocycle` instructions will be executed on a Bio-Rad CFX96 or CFX384 system depending on the plate type used. The per minute costs are tiered, depending on your use of the quantitation system. ## Standard Operation The average ramp rate of the CFX thermocyclers is 3.3°C with a maximum of 5°C. Gradients can be run from 30°C to 100°C with a total temperature span between 1°C and 24°C. The temperature accuracy has been determined to be ±0.2°C of the target temperature with a well-to-well uniformity of ±0.4°C within 10 seconds of arriving at the target temperature. ## Optics The optics use 6 filtered LEDs and photodiodes. Using LEDs provides some major advantages over lamp-based systems. Lamp-based systems are passive and as such the light path lengths is different for every well. A well with a shorter light path will have a higher fluorescence reading compared to a well with a longer path. To compensate for this effect the data has to be normalized by a reference dye. The LED based system does not require that, as the LEDs are positioned directly over each well - resulting in equal length light path. More details on the devices can be found on the [Bio-Rad website](http://www.bio-rad.com/en-us/product/cfx96-touch-real-time-pcr-detection-system).