scinote-web/app/assets/templates/experiment_423/experiment.json

{"experiment":{"id":423,"name":"Antibody Purification","description":"Antibody purification involves selective enrichment or specific isolation of antibodies from serum, ascites fluid or cell culture supernatant of a hybridoma cell line. Purification methods range from very crude to highly specific.\r\nOnce they are purified (and possibly after labelling them with an enzyme or fluorescent tag), these antibodies can be used directly to probe the specific antigen in Western blotting, ELISA and other applications.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:48.389Z","updated_at":"2018-12-21T13:26:16.207Z","workflowimg_file_name":"wimg20181221-1-12rsihs.png","workflowimg_content_type":"image/png","workflowimg_file_size":1460,"workflowimg_updated_at":"2018-12-21T13:26:16.207Z","uuid":"37198411-2ad0-4198-b680-47f3b455ce0d"},"my_modules":[{"my_module":{"id":2097,"name":"Polishing","due_date":null,"description":null,"x":72,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.322Z","updated_at":"2018-12-21T13:25:20.391Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6024,"input_id":2098,"output_id":2097}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3407,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2097,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.390Z","updated_at":"2019-02-20T07:39:44.494Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4287,"name":"Before applying a new sample","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRe-equilibrate column with buffer until the baseline of the monitored signal is stable. Proteins can be monitored at\u003cstrong\u003e 280 nm.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.408Z","updated_at":"2018-12-21T13:31:50.804Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4290,"name":"Polishing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eEquilibrate with 2 column volumes of the buffer\u003c/strong\u003e at a recommended flow rate (See the table). Apply a sample volume equivalent to between \u003cstrong\u003e0.3%\u003c/strong\u003e and \u003cstrong\u003e4%\u003c/strong\u003e of the bed volume. For most applications, the sample volume should not exceed \u003cstrong\u003e2%\u003c/strong\u003e to achieve high resolution. Smaller sample volumes generally lead to an improved resolution. \u003cbr\u003e\u003cstrong\u003eElute with 1 column volume of buffer solution\u003c/strong\u003e (\u003cstrong\u003e10\u003c/strong\u003e to \u003cstrong\u003e50 mM\u003c/strong\u003e sodium phosphate, \u003cstrong\u003e150 mM\u003c/strong\u003e sodium chloride, \u003cstrong\u003epH 7.0\u003c/strong\u003e to \u003cstrong\u003e7.4\u003c/strong\u003e, or select the buffer in which the sample should be stored or solubilized for the next step). The sample should be fully dissolved. Centrifuge or filter to remove particulate matter.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.496Z","updated_at":"2019-02-07T10:46:31.811Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":439,"step_id":4290,"table_id":555}],"tables":[{"id":555,"created_at":"2018-11-08T10:28:49.522Z","updated_at":"2019-02-07T10:46:31.797Z","created_by_id":202,"last_modified_by_id":202,"name":"Separation options","team_id":1,"contents":"eyJkYXRhIjpbWyJGcmFjdGlvbmF0aW9uIHJhbmdlLCBNciAoZ2xvYnVsYXIg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\nIDUwICIsIjIiLCIwLDA3NSJdXX0=\n","data_vector":"JzAnOjM3LDUyLDY3LDgyLDk3LDExMiwxMjcsMTQyICcwNzUnOjUzLDE0MyAn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\nLDExOCwxMjQsMTMzLDEzOSAndHlwaWNhbCc6MTEgJ3ZvbHVtZSc6Nw==\n"}]},{"step":{"id":5224,"name":"For the first time use","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eRemove storage solution. Applying \u003cstrong\u003e2 column\u003c/strong\u003e volume of distilled water at room temperature. Use a low flow rate to avoid gap formation. Perform a column performance test (see below) and \u003cstrong\u003edetermine the limit for maximum pressure over the packed bed is recommended.\u003c/strong\u003e If this has already been done, go to \u003cstrong\u003eStep 2.\u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eColumn efficiency test (the efficiency and peak asymmetry can be determined as follows): \u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\n\u003c/div\u003e\n\u003col\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eEquilibrate the packed column in distilled water or buffer at the flow rate recommended in the product instructions. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eInject \u003cstrong\u003e2%\u003c/strong\u003e acetone (\u003cstrong\u003e20mg/mL\u003c/strong\u003e in water) in a volume equivalent to \u003cstrong\u003e0.2%\u003c/strong\u003e to \u003cstrong\u003e0.4%\u003c/strong\u003e of the geometrical bed volume. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eMonitor UV absorbance at 280 nm and determine the elution volume for acetone. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003e\n\u003cstrong\u003eCalculate column efficiency\u003c/strong\u003e, that is, the number of theoretical plates per meter (N/m). \u003cstrong\u003eN/m= 5.54 x (\u003cspan style=\"color: inherit; font-size: inherit;\"\u003eVe x \u003c/span\u003eW\u003csub\u003e1/2\u003c/sub\u003e)\u003csup\u003e2\u003c/sup\u003e x 1/L\u003c/strong\u003e ; where V\u003csub\u003ee\u003c/sub\u003e =peak elution (retention) volume; W\u003csub\u003e1/2\u003c/sub\u003e=peak width at half peak height; L= bed height (m)\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cstrong\u003eCalculate the asymmetry factor\u003c/strong\u003e A\u003csub\u003es\u003c/sub\u003e= b/a; where a=first half width at \u003cstrong\u003e10%\u003c/strong\u003e peak height and b=second half width at \u003cstrong\u003e10%\u003c/strong\u003e peak height\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T07:24:14.116Z","updated_at":"2019-02-20T07:40:29.217Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[{"id":3092,"step_id":5224,"asset_id":3754}],"assets":[{"id":3754,"created_at":"2019-02-20T07:39:44.265Z","updated_at":"2019-02-20T07:40:29.203Z","file_file_name":"Column_efficiency.jpg","file_content_type":"image/jpeg","file_file_size":11210,"file_updated_at":"2019-02-20T07:40:28.800Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":12331,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2096,"name":"Capture","due_date":null,"description":null,"x":36,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:48.971Z","updated_at":"2018-12-21T13:25:20.382Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6023,"input_id":2097,"output_id":2096}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3405,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2096,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.025Z","updated_at":"2019-02-19T14:49:30.738Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4286,"name":"Preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the preparation guidelines for capture task.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.261Z","updated_at":"2018-12-24T09:19:05.983Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[{"checklist":{"id":968,"name":"Guideline:","step_id":4286,"created_at":"2018-12-21T13:27:09.411Z","updated_at":"2018-12-21T13:27:09.411Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3984,"text":"Equilibrate all materials to the temperature at which the separation will be performed.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.413Z","updated_at":"2018-12-21T13:27:09.413Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3985,"text":"Eliminate air by flushing column end pieces with buffer. Ensure no air is trapped under the column net. Close column outlet leaving 1–2 cm of the buffer in the column.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.421Z","updated_at":"2018-12-21T13:27:09.421Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3986,"text":"Gently resuspend the medium. For media not supplied in suspension, use a medium: buffer ratio of approximately 1:2 to produce a suspension for mixing during rehydration. Avoid using magnetic stirrers since they may damage the matrix.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.427Z","updated_at":"2018-12-21T13:27:09.427Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4279,"name":"Stop the pump and close the column outlet.","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eRemove the top piece and carefully fill the rest of the column with buffer to form an upward meniscus at the top. Insert the adaptor into the column at an angle, ensuring that no air is trapped under the net. Slide the adaptor slowly down the column (the outlet of the adaptor should be open) until the mark is reached. Lock the adaptor in position. Connect the column to the pump and begin equilibration. Re-position the adaptor if necessary.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.069Z","updated_at":"2018-12-21T13:29:08.411Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4283,"name":"Column fill and setting the column outlet.","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eEstimate the amount of resuspended medium required and our the required volume of the medium into the column. Pouring down a glass rod held against the wall of the column will minimize the introduction of air bubbles. \u003cstrong\u003eImmediately fill the column with buffer\u003c/strong\u003e. Mount the column top piece and connect to a pump. Open the column outlet and set the pump to the desired flow rate. If the recommended flow rate cannot be obtained, use the maximum flow rate the pump can deliver. \u003cstrong\u003eDo not exceed the maximum operating pressure of the medium or column.\u003c/strong\u003e Maintain the packing flow rate for at least \u003cstrong\u003e3 column volumes\u003c/strong\u003e after a constant bed height is obtained. Mark the bed height on the column. Do not exceed \u003cstrong\u003e75%\u003c/strong\u003e of the packing flow rate during any purification.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.179Z","updated_at":"2019-02-19T14:49:30.685Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2095,"name":"Buffer exchange and desalting","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:48.686Z","updated_at":"2018-12-21T13:25:20.385Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6022,"input_id":2096,"output_id":2095}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3403,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2095,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:48.743Z","updated_at":"2019-02-20T07:39:23.923Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4273,"name":"Buffer exchange and desalting","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eFill the syringe with buffer.\u003c/strong\u003e To avoid introducing air into the column, connect the column \"drop to drop\" to the syringe (via the adapter). Wash the column. Use \u003cstrong\u003e25 mL\u003c/strong\u003e buffer at \u003cstrong\u003e5 mL/min\u003c/strong\u003e to remove completely the \u003cstrong\u003e20%\u003c/strong\u003e ethanol (supplied as storage buffer). If air is trapped in the column, wash with degassed buffer until the air disappears. Air bubbles introduced onto the column by accident during sample application do not influence the separation.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eApplying the sample.\u003c/strong\u003e Use a\u003cstrong\u003e 2–5 mL\u003c/strong\u003e syringe at a flow rate between \u003cstrong\u003e1–10 mL/min\u003c/strong\u003e. Discard the liquid eluted from the column. If the sample volume is less than \u003cstrong\u003e1.5 mL\u003c/strong\u003e, change to buffer and proceed with the injection until a total of \u003cstrong\u003e1.5 mL\u003c/strong\u003e has been eluted. Discard the eluted liquid.pter). Elute the protein with the appropriate volume.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eSelect volume from the table.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:48.761Z","updated_at":"2019-02-20T07:39:28.712Z","last_modified_by_id":202,"protocol_id":3403},"checklists":[],"step_comments":[],"step_assets":[{"id":3091,"step_id":4273,"asset_id":3753}],"assets":[{"id":3753,"created_at":"2019-02-20T07:39:23.642Z","updated_at":"2019-02-20T07:39:28.703Z","file_file_name":"Desalting_and_Buffer_Exchange.jpg","file_content_type":"image/jpeg","file_file_size":26888,"file_updated_at":"2019-02-20T07:39:28.205Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":29576,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[{"id":438,"step_id":4273,"table_id":554}],"tables":[{"id":554,"created_at":"2018-11-08T10:28:48.787Z","updated_at":"2018-12-20T13:33:54.646Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJTYW1wbGUgbG9hZCAobUwpIiwiQWRkIGJ1ZmZlciAobUwp\nIiwiRWx1dGUgYW5kIGNvbGxlY3QgKG1MKSIsIllpZWxkICglKSIsIlJlbWFp\nbmluZyBzYWx0ICglKSIsIkRpbHV0aW9uIGZhY3RvciAoJSkiXSxbIjAsMjUi\nLCIxLDI1IiwiMSwwIiwiPjk1IiwiMCwwIiwiNCwwIl0sWyIwLDUwIiwiMSww\nIiwiMSw1IiwiPjk1IiwiPDAsMSIsIjMsMCJdLFsiMSwwMCIsIjAsNSIsIjIs\nMCIsIj45NSIsIjwwLDIiLCIyLDAiXSxbIjEsNTAiLCIwIiwiMiwwIiwiPjk1\nIiwiPDAsMiIsIjEsMyJdXX0=\n","data_vector":"JzAnOjE2LDIxLDIzLDI0LDI2LDI3LDMwLDM0LDM3LDQwLDQzLDQ1LDQ4LDUx\nLDUzLDU1ICcwMCc6MzkgJzEnOjE4LDIwLDI5LDMxLDM1LDM4LDQ5LDU3ICcy\nJzo0Miw0Niw0Nyw1Miw1NiAnMjUnOjE3LDE5ICczJzozNiw1OCAnNCc6MjUg\nJzUnOjMyLDQxICc1MCc6MjgsNTAgJzk1JzoyMiwzMyw0NCw1NCAnYWRkJzo0\nICdhbmQnOjggJ2J1ZmZlcic6NSAnY29sbGVjdCc6OSAnZGlsdXRpb24nOjE0\nICdlbHV0ZSc6NyAnZmFjdG9yJzoxNSAnbG9hZCc6MiAnbWwnOjMsNiwxMCAn\ncmVtYWluaW5nJzoxMiAnc2FsdCc6MTMgJ3NhbXBsZSc6MSAneWllbGQnOjEx\n"}]},{"step":{"id":5209,"name":"Centrifuge set up","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow guidelines for centrifuge set up.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-18T14:10:46.319Z","updated_at":"2018-12-24T09:16:18.589Z","last_modified_by_id":202,"protocol_id":3403},"checklists":[{"checklist":{"id":934,"name":"Before use:","step_id":5209,"created_at":"2018-12-18T14:10:46.321Z","updated_at":"2018-12-18T14:10:46.321Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3838,"text":"Check the inside of the centrifuge and the rotors to ensure that everything is dry.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.323Z","updated_at":"2018-12-21T12:47:12.263Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3839,"text":"Check that shock-absorbing pads are in the bottom of the centrifuge buckets.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.331Z","updated_at":"2018-12-18T14:10:46.331Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3840,"text":"Balance the opposing buckets by weighing them with their tubes on an open two-pan balance.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.337Z","updated_at":"2018-12-18T14:10:46.337Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3841,"text":"Never fill centrifuge tubes to more than three-quarters capacity.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.344Z","updated_at":"2018-12-18T14:10:46.344Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3842,"text":"Symmetrically distribute balanced tubes in opposing buckets. Always operate the centrifuge with all buckets in place, even if two opposing buckets are empty.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.354Z","updated_at":"2018-12-18T14:10:46.354Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5210,"name":"Centrifugation of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eSwitch on and follow the manufacturer's instructions to set the centrifugation conditions.\u003cbr\u003eFor small sample volumes or proteins that adsorb non-specifically to filters, centrifuge at \u003cstrong\u003e10 000 x g\u003c/strong\u003e for \u003cstrong\u003e15 minutes\u003c/strong\u003e. 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Remove the sealed buckets (not tubes) slowly and carefully to prevent re-suspension. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-18T14:12:05.603Z","updated_at":"2019-02-07T10:41:20.533Z","last_modified_by_id":202,"protocol_id":3403},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2098,"name":"Analysis","due_date":null,"description":null,"x":105,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.665Z","updated_at":"2018-12-21T13:25:20.388Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3409,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2098,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.719Z","updated_at":"2018-12-24T09:22:25.677Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5226,"name":"Purity analysis: SDS PAGE","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eSodium dodecyl \u003c/strong\u003e\u003c/em\u003esulfate polyacrylamide\u003cem\u003e\u003cstrong\u003e gel electrophoresis (SDS-PAGE) is a technology commonly used in protein purification and analysis.\u003c/strong\u003e \u003cstrong\u003eSDS-PAGE can separate proteins according to the differences in the charge and the different mobility due to different molecular sizes\u003c/strong\u003e\u003c/em\u003e. If the protein sample has been highly purified and contains only one protein, the results would show a single protein band after SDS-PAGE separation. However, when there are multiple proteins in the protein samples, different proteins can be separated into multiple protein bands through SDS-PAGE. 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Samples are measured according to Mass Spectrometer manual. After the MS data is collected, the next step is to\u003cstrong\u003e perform a database search to identify the proteins and/or peptides analyzed by MS\u003c/strong\u003e. A number of parameters can affect the outcome of a database search, and, ultimately, search parameters should consider the history of the sample, \u003cstrong\u003esuch as organism, enzymatic or chemical digestion, and reduction/alkylation steps\u003c/strong\u003e. Differences among search engines can include the scoring algorithm, whether it considers data quality, and whether it considers all fragment ion types or only a subset. 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protein.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.662Z","updated_at":"2018-12-21T13:35:09.662Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3988,"text":"Dilute protein samples to obtain 5-100 µg protein/30 µL.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.669Z","updated_at":"2018-12-21T13:35:09.669Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3989,"text":"Set two blank tubes. For the standard curve, add 30 µL of water instead of the standard solution. For the unknown protein samples, add 30 µL protein preparation buffer instead. Protein solutions are normally assayed in duplicate or triplicate.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.675Z","updated_at":"2018-12-21T13:35:09.675Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3990,"text":"Add 1.5 mL of Bradford reagent to each tube and mix well.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.682Z","updated_at":"2018-12-21T13:35:09.682Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3991,"text":"Incubate at room temperature for at least 5 min.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.688Z","updated_at":"2018-12-21T13:35:09.688Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3992,"text":"Absorbance will increase over time; samples should incubate at RT for no more than 1 h.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.703Z","updated_at":"2018-12-21T13:35:09.703Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":3993,"text":"Measure absorbance at 595 nm.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.710Z","updated_at":"2018-12-21T13:35:09.710Z","created_by_id":null,"last_modified_by_id":null,"position":6}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1190,"created_at":"2018-12-21T13:25:20.378Z","updated_at":"2018-12-21T13:25:20.378Z","created_by_id":202,"experiment_id":423}]}