scinote-web/app/assets/templates/experiment_422/experiment.json

{"experiment":{"id":422,"name":"CRISPR transformations with Agrobacterium tumefaciens","description":"This template will allow you to do CRISPR transformation of plants with Agrobacterium tumefaciens. The clustered regularly interspaced short palindromic repeats(CRISPR) associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from the bacterial immune system. This technique enables precise genomic modifications in many different organisms and tissues.","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":"2018-11-08T10:28:00.553Z","updated_at":"2019-02-07T14:56:54.966Z","workflowimg_file_name":"wimg20181219-1-1wln20.png","workflowimg_content_type":"image/png","workflowimg_file_size":3309,"workflowimg_updated_at":"2019-02-07T14:56:54.966Z","uuid":"1a3d39cf-ea51-48a8-b622-d7a9492fd1e7"},"my_modules":[{"my_module":{"id":2089,"name":"Design and construction of gene-specific sgRNA","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1182,"created_at":"2018-11-08T10:28:01.009Z","updated_at":"2018-12-19T11:33:27.356Z","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":422,"state":"uncompleted","completed_on":null},"outputs":[{"id":5991,"input_id":2090,"output_id":2089}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3391,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2089,"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":"2018-11-08T10:28:01.077Z","updated_at":"2019-02-20T07:40:35.070Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4261,"name":"Use the online tools","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\u003ePaste selected sequence in the selected online tool. \u003cbr\u003e\u003cbr\u003eParameters that should be considered are:\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003etarget length\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003ethe maximum number of tandemly repeated nucleotides\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eminimum/maximum GC content. \u003c/li\u003e\n\u003c/ul\u003e\nSelect a genome to query for potential off-target recognition and analyze it. Evaluate and prioritize targets using sequence identity as well as off-target sequence identity.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:01.386Z","updated_at":"2018-12-21T13:40:38.295Z","last_modified_by_id":202,"protocol_id":3391},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4571,"name":"Considerations","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\u003eConsider choosing \u003cstrong\u003eseveral different target sites\u003c/strong\u003e, since not all sgRNAs work equally well. \u003cbr\u003eConsider using a \u003cstrong\u003e20 bp target site that also contains a recognition site of a commercially available restriction enzyme\u003c/strong\u003e. The target site of the restriction enzyme should span the site of Cas9 cleavage (\u003cstrong\u003e3 bp\u003c/strong\u003e in front of the PAM). This will allow you to use the restriction enzyme length polymorphism assay to detect mutations in your \u003cem\u003egene of interest.\u003c/em\u003e\u003c/p\u003e\u003c/body\u003e\u00