{
  "experiment": {
    "id": 433,
    "name": "Development of SNP markers panel",
    "description": "This template shows how to generate a SNP markers panel with the preparation of SNP panel.\r\nSingle nucleotide polymorphisms (SNPs) markers are widely used for genomic research and breeding. Development of a panel of diagnostic SNP markers is used for the genotyping as well as the identification of hybrids and interspecies introgression events.",
    "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": "2018-11-12T08:12:09.669Z",
    "updated_at": "2019-02-07T14:44:00.337Z",
    "uuid": "de7f0d1b-f842-440b-a367-a0333a11430c"
  },
  "my_modules": [
    {
      "my_module": {
        "id": 2150,
        "name": "RAD library preparation and sequencing",
        "due_date": null,
        "description": null,
        "x": 34,
        "y": 0,
        "my_module_group_id": 1167,
        "created_at": "2018-11-12T08:39:44.221Z",
        "updated_at": "2018-12-17T07:51:25.145Z",
        "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,
        "workflow_order": 1,
        "experiment_id": 433,
        "state": "uncompleted",
        "completed_on": null
      },
      "outputs": [
        {
          "id": 5924,
          "input_id": 2151,
          "output_id": 2150
        }
      ],
      "my_module_tags": [

      ],
      "task_comments": [

      ],
      "my_module_repository_rows": [

      ],
      "user_my_modules": [

      ],
      "protocols": [
        {
          "protocol": {
            "id": 3488,
            "name": null,
            "authors": null,
            "description": null,
            "added_by_id": null,
            "my_module_id": 2150,
            "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": "2018-11-12T08:39:44.225Z",
            "updated_at": "2019-02-20T07:58:51.770Z",
            "published_on": null,
            "nr_of_linked_children": 0
          },
          "protocol_protocol_keywords": [

          ],
          "steps": [
            {
              "step": {
                "id": 5192,
                "name": "PCR genotyping",
                "position": 0,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-12-17T07:34:16.845Z",
                "updated_at": "2019-02-19T14:35:53.498Z",
                "last_modified_by_id": 202,
                "protocol_id": 3488
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>PCR conditions: </p>\n<ul>\n<li>95°C for 1 min</li>\n<li>35 cycles: 95°C for 15 s</li>\n<li>56°C for 15 s</li>\n<li>72°C for 22 s</li>\n</ul>\n<br>PCR products run at <strong>60 V</strong> for <strong>40 mins</strong> on a<strong> 2%</strong> agarose gel (<strong>0.5× TAE</strong>, stained with <strong>100 ng/μL</strong> EtBr).</body></html>"
                  },
                  "position": 0
                },
                {
                  "table": {
                    "id": 668,
                    "created_at": "2018-12-17T07:35:02.552Z",
                    "updated_at": "2019-02-19T14:35:53.484Z",
                    "created_by_id": 202,
                    "last_modified_by_id": 202,
                    "name": "PCR Mastermix",
                    "team_id": 1,
                    "contents": "eyJkYXRhIjpbWyJDb21wb25lbnQiLCJWb2x1bWUgKMK1bCkiLCJGaW5hbCBD\nb25jLiJdLFsiTXlUYXEgbWl4IiwiMyIsIjF4Il0sWyJGb3J3YXJkIHByaW1l\nciIsIjAsNCIsIjEwIM68TSJdLFsiUmV2ZXJzZSBwcmltZXIiLCIwLDQiLCIx\nMCDOvE0iXSxbIlRlbXBsYXRlIEROQSIsIjAsNSIsIjXigJM1MCBuZy/OvEwi\nXSxbIlVsdHJhcHVyZSB3YXRlciIsIjEsNyIsIiJdXX0=\n",
                    "data_vector": "JzAnOjEzLDIwLDI3ICcxJzozOCAnMTAnOjE1LDIyICcxeCc6MTAgJzIwMCc6\nMzEgJzIyMzUwJzozMiAnMjY1bCc6NCAnMjc0bCc6MzUgJzI3NG0nOjE3LDI0\nICczJzo5ICczMDInOjMgJzMxNic6MTYsMjMsMzQgJzM0Mic6MzAgJzQnOjE0\nLDIxICc1JzoyOCwyOSAnNyc6MzkgJ2NvbXBvbmVudCc6MSAnY29uYyc6NiAn\nZG5hJzoyNiAnZmluYWwnOjUgJ2ZvcndhcmQnOjExICdtaXgnOjggJ215dGFx\nJzo3ICduZyc6MzMgJ3ByaW1lcic6MTIsMTkgJ3JldmVyc2UnOjE4ICd0ZW1w\nbGF0ZSc6MjUgJ3VsdHJhcHVyZSc6MzYgJ3ZvbHVtZSc6MiAnd2F0ZXInOjM3\n"
                  },
                  "position": 1
                }
              ]
            },
            {
              "step": {
                "id": 4422,
                "name": "Shearing and size selection",
                "position": 2,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T14:41:18.099Z",
                "updated_at": "2019-02-20T07:37:25.765Z",
                "last_modified_by_id": 202,
                "protocol_id": 3488
              },
              "step_comments": [

              ],
              "assets": [
                {
                  "asset": {
                    "id": 3746,
                    "created_at": "2019-02-20T07:36:46.773Z",
                    "updated_at": "2019-02-20T07:37:25.383Z",
                    "created_by_id": 202,
                    "last_modified_by_id": null,
                    "estimated_size": 19765,
                    "lock": null,
                    "lock_ttl": null,
                    "version": 1,
                    "file_processing": false,
                    "team_id": 1
                  },
                  "asset_blob": {
                    "filename": "Shearing.jpg"
                  }
                },
                {
                  "asset": {
                    "id": 3747,
                    "created_at": "2019-02-20T07:36:46.946Z",
                    "updated_at": "2019-02-20T07:37:25.757Z",
                    "created_by_id": 202,
                    "last_modified_by_id": null,
                    "estimated_size": 16540,
                    "lock": null,
                    "lock_ttl": null,
                    "version": 1,
                    "file_processing": false,
                    "team_id": 1
                  },
                  "asset_blob": {
                    "filename": "Amplification.jpg"
                  }
                }
              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Libraries can be quantified by fluorimetry and calibrated by sequencing. </p></body></html>"
                  },
                  "position": 0
                },
                {
                  "checklist": {
                    "checklist": {
                      "id": 960,
                      "name": "Guidelines:",
                      "step_id": 4422,
                      "created_at": "2018-12-21T10:22:55.963Z",
                      "updated_at": "2018-12-21T10:22:55.963Z",
                      "created_by_id": null,
                      "last_modified_by_id": null
                    },
                    "checklist_items": [
                      {
                        "id": 3950,
                        "text": "Size selection (100 to 800 bp) by agarose gel electrophoresis.",
                        "checked": false,
                        "checklist_id": 960,
                        "created_at": "2018-12-21T10:22:55.965Z",
                        "updated_at": "2018-12-21T10:22:55.965Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 0
                      },
                      {
                        "id": 3951,
                        "text": "Gel purification, end repair, dA overhang addition, P2 paired-end adapter ligation and library amplification.",
                        "checked": false,
                        "checklist_id": 960,
                        "created_at": "2018-12-21T10:22:55.972Z",
                        "updated_at": "2018-12-21T10:22:55.972Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 1
                      },
                      {
                        "id": 3952,
                        "text": "120 μL of each amplified library is size-selected (about 250 to 500 bp) by gel electrophoresis.",
                        "checked": false,
                        "checklist_id": 960,
                        "created_at": "2018-12-21T10:22:55.981Z",
                        "updated_at": "2018-12-21T10:22:55.981Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 2
                      },
                      {
                        "id": 3953,
                        "text": "Final libraries are put through quality control and high-throughput sequencing.",
                        "checked": false,
                        "checklist_id": 960,
                        "created_at": "2018-12-21T10:22:55.989Z",
                        "updated_at": "2018-12-21T10:23:18.774Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 3
                      }
                    ]
                  },
                  "position": 1
                }
              ]
            },
            {
              "step": {
                "id": 4420,
                "name": "RAD library preparation",
                "position": 1,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T14:34:29.463Z",
                "updated_at": "2019-02-20T07:58:51.732Z",
                "last_modified_by_id": 202,
                "protocol_id": 3488
              },
              "step_comments": [

              ],
              "assets": [
                {
                  "asset": {
                    "id": 3745,
                    "created_at": "2019-02-20T07:36:16.089Z",
                    "updated_at": "2019-02-20T07:58:51.655Z",
                    "created_by_id": 202,
                    "last_modified_by_id": 202,
                    "estimated_size": 16298,
                    "lock": null,
                    "lock_ttl": null,
                    "version": 1,
                    "file_processing": false,
                    "team_id": 1
                  },
                  "asset_blob": {
                    "filename": "Digestion_of_DNA.jpg"
                  }
                }
              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p> The RAD library was prepared as originally described in <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/18852878/\" target=\"_blank\" rel=\"noopener\">article</a>.<br><br>At least <strong>30</strong> specimens need to be chosen.<br><br><strong>Each sample is digested at 37°C for 40 min with restriction enzyme:</strong></p>\n<ul>\n<li>\n<strong>6 U</strong> <em>restriction enzyme</em> per μg genomic DNA in <strong>1×</strong> Reaction Buffer 4 at a final concentration of about <strong>1 μg</strong> DNA per <strong>50 μL</strong> reaction volume</li>\n<li>The samples are heat-inactivated at <strong>65°C</strong> for <strong>20 min</strong>.</li>\n</ul>\n<br><strong>Individual-specific P1 adapters, each with a unique 5 or 7 bp barcode is ligated to the digested DNA at 22°C for 15 min by adding:</strong><br><br>\n<ul>\n<li>0.6 μL (DNA samples) 100 nmol/L P1 adapter</li>\n<li>0.15 μL 100 mmol/L rATP </li>\n<li>0.25 μL 10× Reaction Buffer 2</li>\n<li>0.125 μL T4 ligase </li>\n<li>reaction volumes made up to 15 μL with nuclease-free water </li>\n</ul>\n<br>After heat-inactivation, the ligation reactions are slowly cooled to room temperature then combined in appropriate multiplex pools.</body></html>"
                  },
                  "position": 0
                }
              ]
            }
          ]
        }
      ],
      "results": [

      ]
    },
    {
      "my_module": {
        "id": 2151,
        "name": "Genotyping RAD alleles",
        "due_date": null,
        "description": null,
        "x": 68,
        "y": 0,
        "my_module_group_id": 1167,
        "created_at": "2018-11-12T08:39:44.243Z",
        "updated_at": "2018-12-17T07:51:25.147Z",
        "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,
        "workflow_order": 2,
        "experiment_id": 433,
        "state": "uncompleted",
        "completed_on": null
      },
      "outputs": [
        {
          "id": 5925,
          "input_id": 2154,
          "output_id": 2151
        }
      ],
      "my_module_tags": [

      ],
      "task_comments": [

      ],
      "my_module_repository_rows": [

      ],
      "user_my_modules": [

      ],
      "protocols": [
        {
          "protocol": {
            "id": 3489,
            "name": null,
            "authors": null,
            "description": null,
            "added_by_id": null,
            "my_module_id": 2151,
            "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": "2018-11-12T08:39:44.247Z",
            "updated_at": "2018-12-21T10:26:41.366Z",
            "published_on": null,
            "nr_of_linked_children": 0
          },
          "protocol_protocol_keywords": [

          ],
          "steps": [
            {
              "step": {
                "id": 4424,
                "name": "RAD markers",
                "position": 0,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T14:59:18.147Z",
                "updated_at": "2018-12-21T10:25:44.853Z",
                "last_modified_by_id": 202,
                "protocol_id": 3489
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>Reads of low quality must be discarded. <br>Retained reads are sorted into loci and genotypes using software developed for that purpose. It will assigns loci using a likelihood-based algorithm to separate actual SNPs from SNPs likely to have arisen from sequencing error. <br><br><strong>Parameters:</strong><br>\n</p>\n<ul>\n<li>De novo assembly parameters.</li>\n<li>Minimum stack depth of 5.</li>\n<li>Maximum of 2 mismatches.</li>\n<li>No more than 1 mismatch between alleles.</li>\n</ul>\n</body></html>"
                  },
                  "position": 0
                }
              ]
            },
            {
              "step": {
                "id": 5194,
                "name": "RAD library construction",
                "position": 1,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-12-17T07:50:46.898Z",
                "updated_at": "2018-12-21T10:26:41.233Z",
                "last_modified_by_id": 202,
                "protocol_id": 3489
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Sequencing data from filtered Informative RAD markers is combined into a single alignment of alleles in RAD library construction. Data analysis is carried out using R and an associated R/<em>adegenet</em> package for Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC).<em><strong> PCA creates simplified models of the total variation within the dataset.</strong> <strong>DAPC identifies clusters of genetically related individuals.</strong></em></p></body></html>"
                  },
                  "position": 0
                }
              ]
            }
          ]
        }
      ],
      "results": [

      ]
    },
    {
      "my_module": {
        "id": 2154,
        "name": "SNP-assay design",
        "due_date": null,
        "description": null,
        "x": 102,
        "y": 0,
        "my_module_group_id": 1167,
        "created_at": "2018-11-12T08:39:44.312Z",
        "updated_at": "2018-12-17T07:51:25.150Z",
        "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,
        "workflow_order": 3,
        "experiment_id": 433,
        "state": "uncompleted",
        "completed_on": null
      },
      "outputs": [

      ],
      "my_module_tags": [

      ],
      "task_comments": [

      ],
      "my_module_repository_rows": [

      ],
      "user_my_modules": [

      ],
      "protocols": [
        {
          "protocol": {
            "id": 3492,
            "name": null,
            "authors": null,
            "description": null,
            "added_by_id": null,
            "my_module_id": 2154,
            "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": "2018-11-12T08:39:44.325Z",
            "updated_at": "2019-02-20T07:37:09.688Z",
            "published_on": null,
            "nr_of_linked_children": 0
          },
          "protocol_protocol_keywords": [

          ],
          "steps": [
            {
              "step": {
                "id": 4428,
                "name": "Genotype assignment",
                "position": 1,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T15:22:18.606Z",
                "updated_at": "2018-11-12T15:22:18.606Z",
                "last_modified_by_id": 202,
                "protocol_id": 3492
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Reading the fluorescence emission of the FAM and HEX fluorophores for each sample, in comparison to no-template control reactions, using a Real Time PCR Thermal Cycler and Quansoft endpoint genotyping software.</p></body></html>"
                  },
                  "position": 0
                }
              ]
            },
            {
              "step": {
                "id": 4427,
                "name": "SNP assays",
                "position": 0,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T15:20:06.636Z",
                "updated_at": "2019-02-20T07:37:26.227Z",
                "last_modified_by_id": 202,
                "protocol_id": 3492
              },
              "step_comments": [

              ],
              "assets": [
                {
                  "asset": {
                    "id": 3748,
                    "created_at": "2019-02-20T07:37:09.362Z",
                    "updated_at": "2019-02-20T07:37:26.219Z",
                    "created_by_id": 202,
                    "last_modified_by_id": null,
                    "estimated_size": 24074,
                    "lock": null,
                    "lock_ttl": null,
                    "version": 1,
                    "file_processing": false,
                    "team_id": 1
                  },
                  "asset_blob": {
                    "filename": "SNP_marker.jpg"
                  }
                }
              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>SNP of interest at a given locus need to be at least <strong>20 bp</strong> from the end of a given sequence, to allow for primer design. SNP assays were designed and manufactured for use with KASP genotyping technology.<br><br><strong>Optimisation assay conditions:</strong></p>\n<ul>\n<li>94°C for 15 min;</li>\n<li>10 cycles 94°C for 20 s, 61–55°C for 120 s (0.6°C drop per cycle)</li>\n<li>40 cycles 94°C for 20 s, 55°C for 120 s </li>\n</ul>\n</body></html>"
                  },
                  "position": 0
                },
                {
                  "table": {
                    "id": 573,
                    "created_at": "2018-11-12T15:20:07.148Z",
                    "updated_at": "2019-02-20T07:37:09.513Z",
                    "created_by_id": 202,
                    "last_modified_by_id": 202,
                    "name": "Reaction mastermix",
                    "team_id": 1,
                    "contents": "eyJkYXRhIjpbWyJDb21wb25lbnQiLCJWb2x1bWUiXSxbIjLDlyBLQVNQIE1h\nc3RlciBNaXgiLCIyLjUgzrxMIl0sWyJLQVNQIEFzc2F5IE1peCIsIjAuMDcg\nzrxMIl0sWyJUZW1wbGF0ZSBETkEiLCIwLjQgzrxMIl0sWyJVbHRyYXB1cmUg\nd2F0ZXIiLCIyLjEgzrxMIl1dfQ==\n",
                    "data_vector": "JzAuMDcnOjE1ICcwLjQnOjIwICcyJzozICcyLjEnOjI1ICcyLjUnOjkgJzIy\nNyc6NSAnMjc0bCc6MTEsMTcsMjIsMjcgJzMwMyc6NCAnMzE2JzoxMCwxNiwy\nMSwyNiAnYXNzYXknOjEzICdjb21wb25lbnQnOjEgJ2RuYSc6MTkgJ2thc3An\nOjYsMTIgJ21hc3Rlcic6NyAnbWl4Jzo4LDE0ICd0ZW1wbGF0ZSc6MTggJ3Vs\ndHJhcHVyZSc6MjMgJ3ZvbHVtZSc6MiAnd2F0ZXInOjI0\n"
                  },
                  "position": 1
                }
              ]
            }
          ]
        }
      ],
      "results": [

      ]
    },
    {
      "my_module": {
        "id": 2149,
        "name": "DNA extracting",
        "due_date": null,
        "description": null,
        "x": 0,
        "y": 0,
        "my_module_group_id": 1167,
        "created_at": "2018-11-12T08:39:44.191Z",
        "updated_at": "2018-12-17T07:51:25.152Z",
        "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,
        "workflow_order": 0,
        "experiment_id": 433,
        "state": "uncompleted",
        "completed_on": null
      },
      "outputs": [
        {
          "id": 5923,
          "input_id": 2150,
          "output_id": 2149
        }
      ],
      "my_module_tags": [

      ],
      "task_comments": [

      ],
      "my_module_repository_rows": [

      ],
      "user_my_modules": [

      ],
      "protocols": [
        {
          "protocol": {
            "id": 3487,
            "name": null,
            "authors": null,
            "description": null,
            "added_by_id": null,
            "my_module_id": 2149,
            "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": "2018-11-12T08:39:44.202Z",
            "updated_at": "2019-02-19T14:34:47.554Z",
            "published_on": null,
            "nr_of_linked_children": 0
          },
          "protocol_protocol_keywords": [

          ],
          "steps": [
            {
              "step": {
                "id": 4416,
                "name": "Protein extraction and RNAse treatment",
                "position": 1,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T12:00:57.856Z",
                "updated_at": "2018-12-24T08:46:24.129Z",
                "last_modified_by_id": 202,
                "protocol_id": 3487
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Here are the guidelines for protein extraction: </p></body></html>"
                  },
                  "position": 0
                },
                {
                  "checklist": {
                    "checklist": {
                      "id": 958,
                      "name": "Guidelines:",
                      "step_id": 4416,
                      "created_at": "2018-12-21T09:50:59.139Z",
                      "updated_at": "2018-12-21T09:50:59.139Z",
                      "created_by_id": null,
                      "last_modified_by_id": null
                    },
                    "checklist_items": [
                      {
                        "id": 3939,
                        "text": "Add 1 volume of chloroform: Isoamyl alcohol to the solution and mix by inversion for 5 min. Centrifuge the sample for 10 min at 5000 × g and pipette the upper aqueous phase into a new Falcon tube.",
                        "checked": false,
                        "checklist_id": 958,
                        "created_at": "2018-12-21T09:50:59.141Z",
                        "updated_at": "2018-12-21T09:50:59.141Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 0
                      },
                      {
                        "id": 3940,
                        "text": "Add 5 μL of RNAse A to the solution and incubate at 37°C for 15 min with periodic, gentle mixing.",
                        "checked": false,
                        "checklist_id": 958,
                        "created_at": "2018-12-21T09:50:59.149Z",
                        "updated_at": "2018-12-21T09:50:59.149Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 1
                      },
                      {
                        "id": 3941,
                        "text": "After incubation, add 1 volume of chloroform: Isoamyl alcohol to the solution and mix by inversion for 5 min.",
                        "checked": false,
                        "checklist_id": 958,
                        "created_at": "2018-12-21T09:50:59.156Z",
                        "updated_at": "2018-12-21T09:50:59.156Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 2
                      },
                      {
                        "id": 3942,
                        "text": "Centrifuge the solution for 10 min at 5000 × g and pipette the aqueous phase into a new Falcon tube.",
                        "checked": false,
                        "checklist_id": 958,
                        "created_at": "2018-12-21T09:50:59.163Z",
                        "updated_at": "2018-12-21T09:50:59.163Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 3
                      }
                    ]
                  },
                  "position": 1
                }
              ]
            },
            {
              "step": {
                "id": 4418,
                "name": "DNA quality and quantity assessment",
                "position": 3,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T12:22:47.725Z",
                "updated_at": "2019-02-19T14:34:47.503Z",
                "last_modified_by_id": 202,
                "protocol_id": 3487
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>Looking for a single absorbance peak at <strong>260 nm</strong>, a <strong>260/280</strong> absorbance ratio of <strong>1.8-2.0</strong> and no evidence of substantial band shearing or contamination (either RNA or polysaccharide).<br><br></p>\n<p><strong>Assess the quality of the extracted DNA:</strong></p>\n<ol>\n<li>NanoDrop UV/Vis spectrophotometer</li>\n<li>0.7% (w/v) agarose gel electrophoresis</li>\n</ol>\n</body></html>"
                  },
                  "position": 0
                }
              ]
            },
            {
              "step": {
                "id": 4414,
                "name": "Preparation",
                "position": 0,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T11:06:48.312Z",
                "updated_at": "2018-12-24T08:34:20.404Z",
                "last_modified_by_id": 202,
                "protocol_id": 3487
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Guidelines for samples preparation below. </p></body></html>"
                  },
                  "position": 0
                },
                {
                  "checklist": {
                    "checklist": {
                      "id": 957,
                      "name": "Guidelines",
                      "step_id": 4414,
                      "created_at": "2018-12-21T09:43:55.386Z",
                      "updated_at": "2018-12-21T09:43:55.386Z",
                      "created_by_id": null,
                      "last_modified_by_id": null
                    },
                    "checklist_items": [
                      {
                        "id": 3934,
                        "text": "Samples are stored in 95% ethanol solution at -20°C.",
                        "checked": false,
                        "checklist_id": 957,
                        "created_at": "2018-12-21T09:43:55.389Z",
                        "updated_at": "2018-12-21T09:43:55.389Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 0
                      },
                      {
                        "id": 3935,
                        "text": "Pre-heat water baths (65°C and 37°C).",
                        "checked": false,
                        "checklist_id": 957,
                        "created_at": "2018-12-21T09:43:55.396Z",
                        "updated_at": "2018-12-21T09:43:55.396Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 1
                      },
                      {
                        "id": 3936,
                        "text": "Prepare 10 mL (per 1 g of sample) extraction buffer by adding 0.3% (v/v) β-mercaptoethanol in a 50 mL Falcon tube, and pre-heat in the 65°C water bath.",
                        "checked": false,
                        "checklist_id": 957,
                        "created_at": "2018-12-21T09:43:55.403Z",
                        "updated_at": "2018-12-21T09:43:55.403Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 2
                      },
                      {
                        "id": 3937,
                        "text": "Put the sample into the 65°C water bath and mix by inversion every 10 min for 30-60 minutes.",
                        "checked": false,
                        "checklist_id": 957,
                        "created_at": "2018-12-21T09:43:55.412Z",
                        "updated_at": "2018-12-21T09:43:55.412Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 3
                      },
                      {
                        "id": 3938,
                        "text": "After incubation, centrifuge the sample tube for 5 min at 5000 × g and decant the supernatant into a new 50 mL Falcon tube.",
                        "checked": false,
                        "checklist_id": 957,
                        "created_at": "2018-12-21T09:43:55.419Z",
                        "updated_at": "2018-12-21T09:43:55.419Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 4
                      }
                    ]
                  },
                  "position": 1
                }
              ]
            },
            {
              "step": {
                "id": 4417,
                "name": "Precipitation",
                "position": 2,
                "completed": false,
                "completed_on": null,
                "user_id": 202,
                "created_at": "2018-11-12T12:05:42.004Z",
                "updated_at": "2019-02-07T10:03:24.266Z",
                "last_modified_by_id": 202,
                "protocol_id": 3487
              },
              "step_comments": [

              ],
              "assets": [

              ],
              "step_orderable_elements": [
                {
                  "step_text": {
                    "text": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>If you are precipitating small volumes of DNA, and you can fit the required amount of solvent into the sample tube, then ice-cold ethanol is the preferred choice. You can chill it (in liquid nitrogen or at <strong>–80°C</strong>) to accelerate the precipitation without the risk of precipitating excess salt. Afterwards, you need to wash the pellet with <strong>70%</strong> ethanol to remove any salt present.</p></body></html>"
                  },
                  "position": 0
                },
                {
                  "checklist": {
                    "checklist": {
                      "id": 959,
                      "name": "Guidelines:",
                      "step_id": 4417,
                      "created_at": "2018-12-21T09:54:21.494Z",
                      "updated_at": "2018-12-21T09:54:21.494Z",
                      "created_by_id": null,
                      "last_modified_by_id": null
                    },
                    "checklist_items": [
                      {
                        "id": 3943,
                        "text": "Add a ½ volume of 5 M NaCl to the sample and mix gently by inversion.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.496Z",
                        "updated_at": "2018-12-21T09:54:21.496Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 0
                      },
                      {
                        "id": 3944,
                        "text": "Then, add 3 volumes of cold 95% ethanol and mix gently by inversion.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.503Z",
                        "updated_at": "2018-12-21T09:54:21.503Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 1
                      },
                      {
                        "id": 3945,
                        "text": "Place the tubes into a -20°C freezer and incubate for 1 h.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.509Z",
                        "updated_at": "2018-12-21T09:54:21.509Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 2
                      },
                      {
                        "id": 3946,
                        "text": "After incubation, centrifuge the Falcon tube for 10 min at 5000 × g to pellet the DNA.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.516Z",
                        "updated_at": "2018-12-21T09:54:21.516Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 3
                      },
                      {
                        "id": 3947,
                        "text": "Carefully decant away the supernatant and wash the DNA pellet with 3 mL of 70% ethanol.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.522Z",
                        "updated_at": "2018-12-21T09:54:21.522Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 4
                      },
                      {
                        "id": 3948,
                        "text": "Gently swirl the solution and centrifuge again for 10 min at 5000 × g.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.529Z",
                        "updated_at": "2018-12-21T09:54:21.529Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 5
                      },
                      {
                        "id": 3949,
                        "text": "Carefully decant the supernatant and air-dry DNA pellet for 15 min at room temperature. Once dried, suspend DNA in 200 μL of TE buffer.",
                        "checked": false,
                        "checklist_id": 959,
                        "created_at": "2018-12-21T09:54:21.535Z",
                        "updated_at": "2018-12-21T09:54:21.535Z",
                        "created_by_id": null,
                        "last_modified_by_id": null,
                        "position": 6
                      }
                    ]
                  },
                  "position": 1
                }
              ]
            }
          ]
        }
      ],
      "results": [

      ]
    }
  ],
  "my_module_groups": [
    {
      "id": 1167,
      "created_at": "2018-12-17T07:51:25.142Z",
      "updated_at": "2018-12-17T07:51:25.142Z",
      "created_by_id": 202,
      "experiment_id": 433
    }
  ]
}