scinote-web/app/assets/templates/experiment_497/experiment.json

{"experiment":{"id":497,"name":"SDS-PAGE for Protein Characterization","description":"This experiment template will help you separate proteins based on their molecular weight. \r\nProteins are separated by electrophoresis through a gel matrix. Smaller proteins migrate faster due to less resistance from the gel matrix. Other influences on the rate of migration through the gel matrix include the structure and charge of the proteins. In SDS-PAGE, the use of sodium dodecyl sulfate (SDS, also known as sodium lauryl sulfate) and polyacrylamide gel largely eliminates the influence of the structure and charge, and proteins are separated solely based on polypeptide chain length.\r\nStaining with Coomassie blue dyes is commonly used to stain proteins and visualize them. But if you want to identify specific proteins (using specific antibodies) a better technique to use is a Western blot.","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":"2018-12-24T10:56:55.416Z","updated_at":"2019-01-28T15:15:24.331Z","workflowimg_file_name":"wimg20181224-1-1hyikrd.png","workflowimg_content_type":"image/png","workflowimg_file_size":2244,"workflowimg_updated_at":"2019-01-28T15:15:24.331Z","uuid":"8aefcdf3-ddb3-4174-8846-129a420426aa"},"my_modules":[{"my_module":{"id":2385,"name":"Preparation of polyacrylamide gel","due_date":null,"description":null,"x":0,"y":7,"my_module_group_id":1195,"created_at":"2018-12-24T11:00:55.170Z","updated_at":"2018-12-24T13:43:31.287Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":497,"state":"uncompleted","completed_on":null},"outputs":[{"id":6050,"input_id":2384,"output_id":2385}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3902,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2385,"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":"2018-12-24T11:00:55.177Z","updated_at":"2019-01-29T10:04:08.808Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5250,"name":"Make the stacking gel","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\u003cp\u003eProteins are highly concentrated when they migrate through a stacking gel prior to entering a separating gel. The concentration occurs due to the difference in the rate of migration of glycine ion, chloride ion, and proteins.\u003cstrong\u003e\u003cbr\u003e\u003cbr\u003e5mL stacking gel:\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eH2O \u003cstrong\u003e2.975 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e0.5 M\u003c/strong\u003e Tris-HCl, \u003cstrong\u003epH 6.8 1.25 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e10%\u003c/strong\u003e (w/v) SDS \u003cstrong\u003e0.05 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003eAcrylamide/Bis-acrylamide (\u003cstrong\u003e30%/0.8% w/v\u003c/strong\u003e) \u003cstrong\u003e0.67 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e10%\u003c/strong\u003e (w/v) ammonium persulfate (AP) \u003cstrong\u003e0.05 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003eTEMED \u003cstrong\u003e0.005 mL\u003c/strong\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003e\u003cstrong\u003e1x Running buffer:\u003cbr\u003e\u003c/strong\u003e\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003e25 mM\u003c/strong\u003e Tris-HCl\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e200 mM\u003c/strong\u003e Glycine\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u0