{"experiment":{"id":422,"name":"CRISPR transformations with Agrobacterium tumefaciens","description":"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":"2018-12-19T11:43:40.164Z","workflowimg_file_name":"wimg20181219-1-1wln20.png","workflowimg_content_type":"image/png","workflowimg_file_size":3309,"workflowimg_updated_at":"2018-12-19T11:43:40.164Z","uuid":"03679cca-2fdc-4df5-8432-8467b6b5152e"},"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,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":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":"2018-12-24T09:25:18.192Z","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 (3 bp 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\u003c/html\u003e","position":2,"completed":false,"com
