{"__v":12,"_id":"5509fd2bdfed731900b81863","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":"54e3d35e464a9c3700f7ca7f","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":"2015-03-18T22:33:15.181Z","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\": \"Instruction and Parameters\"\n}\n[/block]\nThe `flow_analyze` instruction takes parameters to modify and add channels from a list matching the instruments capabilities. For any channel you will have to specify which parameters to collect (`area`,`height`,`width`) and you can suggest a `voltage_range` in which we check for the best resolution and data distribution of your samples. The actual voltage used will be returned to you in the results. \n\nIn addition to general set-up you need to specify at least one negative control and one sample. The negative control is used to set-up the experiment and optimize the voltage for that given channel/color. You may have more than one negative control. Positive controls in this instruction refer to technical positive controls, which may overlap with your biological controls. They are used to determine the maximum expected signal on their given channel, as well as any color bleed that can be later corrected by compensation. \n\nOnly after all negative and positive controls have been run will the samples be analyzed. A well can be used for both control and sample, assuming enough liquid is present. \n\nAny data collection step will be run until the specified `volume` is run or the number of `captured_events` is reached, whichever occurs first. Please note that `volume` is a required parameter and `captured_events` is optional.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"flow_analyze\\\",\\n  \\\"dataref\\\": \\\"flow_data\\\",\\n  \\\"channels\\\": {\\n    \\\"FSC\\\": {\\n      \\\"voltage_range\\\": {\\n        \\\"low\\\": \\\"230:volt\\\",\\n        \\\"high\\\": \\\"280:volt\\\"\\n        },\\n      \\\"area\\\": true,             //default: true\\n      \\\"height\\\": true,           //default: true\\n      \\\"weight\\\": false           //default: false\\n      },\\n    \\\"SSC\\\": {\\n      \\\"voltage_range\\\": { … },\\n      \\\"area\\\": true,             //default: true\\n      \\\"height\\\": false,          //default: false\\n      \\\"weight\\\": false           //default: false\\n      },\\n    \\\"colors\\\":[{\\n      \\\"name\\\": \\\"FitC\\\",\\n      \\\"emission_wavelength\\\": \\\"495:nanometer\\\",\\n      \\\"excitation_wavelength\\\": \\\"519:nanometer\\\",\\n      \\\"voltage_range\\\": { … },\\n      \\\"area\\\": true,             //default: true\\n      \\\"height\\\": false,          //default: false\\n      \\\"weight\\\": false           //default: false\\n    }, … ]\\n  },\\n  \\\"negative_controls\\\": [{\\n    \\\"well\\\": well,\\n    \\\"volume\\\": volume,\\n    \\\"captured_events\\\": integer,     // optional, default infinity\\n    \\\"channel\\\": [channel_name]\\n  }],                               // at least 1 negative control req'd\\n  \\\"positive_controls\\\": [{\\n    \\\"well\\\": well,\\n    \\\"volume\\\": volume,\\n    \\\"captured_events\\\": integer,     // optional, default infinity\\n    \\\"channel\\\": [channel_name],\\n    \\\"minimize_bleed\\\": [{            // optional\\n      \\\"from\\\": color,\\n      \\\"to\\\": [color]\\n    }, … ]\\n  }],\\n  \\\"samples\\\": [{\\n    \\\"well\\\": well,\\n    \\\"volume\\\": volume,\\n    \\\"captured_events\\\": integer,     // optional, default infinity\\n  }]\\n}\",\n      \"language\": \"json\",\n      \"name\": \"flow_analyze\"\n    }\n  ]\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"parameters\\\": {\\n    \\\"FSC_voltage\\\": volt,\\n    \\\"SSC_voltage\\\": volt,\\n    \\\"colors\\\":{[\\n      \\\"name\\\": string,\\n      \\\"actual_voltage\\\": volt\\n    ], … },\\n  }\\n  \\\"data\\\": {\\n    \\\"plate1/A3\\\": {\\n      \\\"fsc_3.1\\\": \\\"url\\\"\\n    }\\n  }\\n}\\n\",\n      \"language\": \"json\",\n      \"name\": \"flow results\"\n    }\n  ]\n}\n[/block]\n## Supported excitation and emission wavelengths\nUse any of the following combinations of excitation and emission wavelength. The `name` can be chosen freely and we recommend to use the name of the dye or fluorescent protein that you are detecting. \nThe name chosen here will be used to determine any specific negative and positive controls.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Laser\",\n    \"h-1\": \"Excitation\",\n    \"h-2\": \"Emission\",\n    \"h-3\": \"Common Dye\",\n    \"0-0\": \"Violet\",\n    \"0-3\": \"Pacific Blue\",\n    \"0-1\": \"405 nm\",\n    \"0-2\": \"440 nm\",\n    \"1-0\": \"Violet\",\n    \"1-1\": \"405 nm\",\n    \"1-2\": \"512 nm\",\n    \"1-3\": \"Pacific Green\",\n    \"2-0\": \"Violet\",\n    \"2-1\": \"405 nm\",\n    \"2-2\": \"603 nm\",\n    \"2-3\": \"Pacific Orange\",\n    \"3-0\": \"Violet\",\n    \"3-1\": \"405 nm\",\n    \"3-2\": \"710 nm\",\n    \"3-3\": \"Qdot 705\",\n    \"4-1\": \"488 nm\",\n    \"4-0\": \"Blue\",\n    \"5-0\": \"Blue\",\n    \"6-0\": \"Blue\",\n    \"5-1\": \"488 nm\",\n    \"6-1\": \"488 nm\",\n    \"4-2\": \"530 nm\",\n    \"5-2\": \"574 nm\",\n    \"6-2\": \"695 nm\",\n    \"4-3\": \"FITC\",\n    \"5-3\": \"Propidium iodide\",\n    \"6-3\": \"PerCP-Cy5.5\",\n    \"7-3\": \"PE\",\n    \"8-3\": \"PE-Texas Red\",\n    \"9-3\": \"PE-Cy5.5\",\n    \"10-3\": \"PE-Cy7\",\n    \"7-0\": \"Yellow\",\n    \"8-0\": \"Yellow\",\n    \"9-0\": \"Yellow\",\n    \"10-0\": \"Yellow\",\n    \"7-1\": \"561 nm\",\n    \"8-1\": \"561 nm\",\n    \"9-1\": \"561 nm\",\n    \"10-1\": \"561 nm\",\n    \"7-2\": \"583 nm\",\n    \"8-2\": \"620 nm\",\n    \"9-2\": \"695 nm\",\n    \"10-2\": \"780 nm\",\n    \"11-0\": \"Red\",\n    \"12-0\": \"Red\",\n    \"13-0\": \"Red\",\n    \"11-1\": \"638 nm\",\n    \"11-2\": \"660 nm\",\n    \"12-1\": \"638 nm\",\n    \"13-1\": \"638 nm\",\n    \"12-2\": \"720 nm\",\n    \"13-2\": \"780 nm\",\n    \"11-3\": \"APC\",\n    \"12-3\": \"Alexa Fluor 700\",\n    \"13-3\": \"APC-Alexa Fluor 750\",\n    \"h-4\": \"Fluorescent protein\",\n    \"0-4\": \"ECFP\",\n    \"4-4\": \"EGFP, Emerald GFP\",\n    \"5-4\": \"EYFP\",\n    \"7-4\": \"RFP\",\n    \"8-4\": \"mCherry, dTomato,  DsRed, mStrawberry\"\n  },\n  \"cols\": 5,\n  \"rows\": 14\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Device\"\n}\n[/block]\nTranscriptic uses the Attune NxT Acoustic Focusing Cytometer equipped with a violet, blue, red and yellow laser. In addition to sheath fluid the Attune uses sound waves to focus your cells, allowing for fast acquisition speeds while maintaining high resolution.\nThe instrument is routinely run at 100uL/min, with flow rates being adjusted to reflect sample quality and complexity. \n\nBefore analysis in the system, every well is mixed 2 times to suspend the cells properly. The sample is not recoverable, meaning if `captured_events` is set and this limit is reached before the entire `volume` of cells has been analyzed, the remaining volume is discarded and not returned to the source plate.","excerpt":"","slug":"flow-analyze","type":"basic","title":"Flow Cytometry"}
[block:api-header] { "type": "basic", "title": "Instruction and Parameters" } [/block] The `flow_analyze` instruction takes parameters to modify and add channels from a list matching the instruments capabilities. For any channel you will have to specify which parameters to collect (`area`,`height`,`width`) and you can suggest a `voltage_range` in which we check for the best resolution and data distribution of your samples. The actual voltage used will be returned to you in the results. In addition to general set-up you need to specify at least one negative control and one sample. The negative control is used to set-up the experiment and optimize the voltage for that given channel/color. You may have more than one negative control. Positive controls in this instruction refer to technical positive controls, which may overlap with your biological controls. They are used to determine the maximum expected signal on their given channel, as well as any color bleed that can be later corrected by compensation. Only after all negative and positive controls have been run will the samples be analyzed. A well can be used for both control and sample, assuming enough liquid is present. Any data collection step will be run until the specified `volume` is run or the number of `captured_events` is reached, whichever occurs first. Please note that `volume` is a required parameter and `captured_events` is optional. [block:code] { "codes": [ { "code": "{\n \"op\": \"flow_analyze\",\n \"dataref\": \"flow_data\",\n \"channels\": {\n \"FSC\": {\n \"voltage_range\": {\n \"low\": \"230:volt\",\n \"high\": \"280:volt\"\n },\n \"area\": true, //default: true\n \"height\": true, //default: true\n \"weight\": false //default: false\n },\n \"SSC\": {\n \"voltage_range\": { … },\n \"area\": true, //default: true\n \"height\": false, //default: false\n \"weight\": false //default: false\n },\n \"colors\":[{\n \"name\": \"FitC\",\n \"emission_wavelength\": \"495:nanometer\",\n \"excitation_wavelength\": \"519:nanometer\",\n \"voltage_range\": { … },\n \"area\": true, //default: true\n \"height\": false, //default: false\n \"weight\": false //default: false\n }, … ]\n },\n \"negative_controls\": [{\n \"well\": well,\n \"volume\": volume,\n \"captured_events\": integer, // optional, default infinity\n \"channel\": [channel_name]\n }], // at least 1 negative control req'd\n \"positive_controls\": [{\n \"well\": well,\n \"volume\": volume,\n \"captured_events\": integer, // optional, default infinity\n \"channel\": [channel_name],\n \"minimize_bleed\": [{ // optional\n \"from\": color,\n \"to\": [color]\n }, … ]\n }],\n \"samples\": [{\n \"well\": well,\n \"volume\": volume,\n \"captured_events\": integer, // optional, default infinity\n }]\n}", "language": "json", "name": "flow_analyze" } ] } [/block] [block:code] { "codes": [ { "code": "{\n \"parameters\": {\n \"FSC_voltage\": volt,\n \"SSC_voltage\": volt,\n \"colors\":{[\n \"name\": string,\n \"actual_voltage\": volt\n ], … },\n }\n \"data\": {\n \"plate1/A3\": {\n \"fsc_3.1\": \"url\"\n }\n }\n}\n", "language": "json", "name": "flow results" } ] } [/block] ## Supported excitation and emission wavelengths Use any of the following combinations of excitation and emission wavelength. The `name` can be chosen freely and we recommend to use the name of the dye or fluorescent protein that you are detecting. The name chosen here will be used to determine any specific negative and positive controls. [block:parameters] { "data": { "h-0": "Laser", "h-1": "Excitation", "h-2": "Emission", "h-3": "Common Dye", "0-0": "Violet", "0-3": "Pacific Blue", "0-1": "405 nm", "0-2": "440 nm", "1-0": "Violet", "1-1": "405 nm", "1-2": "512 nm", "1-3": "Pacific Green", "2-0": "Violet", "2-1": "405 nm", "2-2": "603 nm", "2-3": "Pacific Orange", "3-0": "Violet", "3-1": "405 nm", "3-2": "710 nm", "3-3": "Qdot 705", "4-1": "488 nm", "4-0": "Blue", "5-0": "Blue", "6-0": "Blue", "5-1": "488 nm", "6-1": "488 nm", "4-2": "530 nm", "5-2": "574 nm", "6-2": "695 nm", "4-3": "FITC", "5-3": "Propidium iodide", "6-3": "PerCP-Cy5.5", "7-3": "PE", "8-3": "PE-Texas Red", "9-3": "PE-Cy5.5", "10-3": "PE-Cy7", "7-0": "Yellow", "8-0": "Yellow", "9-0": "Yellow", "10-0": "Yellow", "7-1": "561 nm", "8-1": "561 nm", "9-1": "561 nm", "10-1": "561 nm", "7-2": "583 nm", "8-2": "620 nm", "9-2": "695 nm", "10-2": "780 nm", "11-0": "Red", "12-0": "Red", "13-0": "Red", "11-1": "638 nm", "11-2": "660 nm", "12-1": "638 nm", "13-1": "638 nm", "12-2": "720 nm", "13-2": "780 nm", "11-3": "APC", "12-3": "Alexa Fluor 700", "13-3": "APC-Alexa Fluor 750", "h-4": "Fluorescent protein", "0-4": "ECFP", "4-4": "EGFP, Emerald GFP", "5-4": "EYFP", "7-4": "RFP", "8-4": "mCherry, dTomato, DsRed, mStrawberry" }, "cols": 5, "rows": 14 } [/block] [block:api-header] { "type": "basic", "title": "Device" } [/block] Transcriptic uses the Attune NxT Acoustic Focusing Cytometer equipped with a violet, blue, red and yellow laser. In addition to sheath fluid the Attune uses sound waves to focus your cells, allowing for fast acquisition speeds while maintaining high resolution. The instrument is routinely run at 100uL/min, with flow rates being adjusted to reflect sample quality and complexity. Before analysis in the system, every well is mixed 2 times to suspend the cells properly. The sample is not recoverable, meaning if `captured_events` is set and this limit is reached before the entire `volume` of cells has been analyzed, the remaining volume is discarded and not returned to the source plate.