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@Longlius
Created February 16, 2017 16:01
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An example of protocols.io JSON output with steps included.
{
"api_version": "1",
"is_new_mode": "1",
"protocol_name": "Transformation of Skeletonema marinoi using Multipulse Electroporation",
"last_modified": "1487254340",
"type_id": "1",
"link": "",
"fork_id": "",
"public_fork_note": "",
"number_of_steps": "7",
"uri": "transformation-of-skeletonema-marinoi-using-multip-g6nbzde",
"has_versions": "0",
"first_published_date": "2017-02-10 10:06:56",
"publish_date": "2017-02-10 10:06:56",
"documents": null,
"have_protocol_in_step": "0",
"is_protocol_in_step": "0",
"vendor_name": "Contributed by users",
"vendor_link": "https://www.protocols.io",
"vendor_logo": "/img/vendors/1.png",
"mod_mins": "-34",
"mod_secs": "34",
"description": "<p><em>The following transformation protocol is designed for the insertion of linear DNA constructs into the nuclear genome of Skeletonema marinoi by non-homologous recombination.</em></p>",
"is_bookmarked": "0",
"can_reassign": "0",
"before_start": "",
"has_guidelines": "0",
"materials": null,
"warning": "",
"is_prepublished": "0",
"public": "1",
"is_owner": "0",
"is_original_owner": "0",
"created_on": "1486720407",
"authors": "Oskar N. Johansson., Adrian K. Clarke",
"protocol_affiliation": "BioEnv - University of Gothenburg",
"steps": [
{
"id": "319256",
"is_changed": "0",
"original_id": "0",
"guid": "3A674EEDAB454907BEAB82DCDE053595",
"previous_guid": null,
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>a) Grow two 400 mL cultures in Artificial Seawater with f/2+Si supplements (Growth media) for ca. one week until dense. The standard growth conditions used in our lab are 16°C, 50-70 µmol. photons m-2 s-1, 16 h photoperiod.</p>\n<p>b) Reduce the volume of the sedimented culture in each flask to 50 mL by suction. Resuspend cells by vigorous agitation to minimize chain length and then transfer them to a 50 mL centrifuge tube.</p>\n<p>c) Pellet cells by centrifugation (1200 x g, 5 min, 4°C, swing-out rotor). Decant supernatant and resuspend the pellet in each tube in 10 mL of ice-cold 0.3M sorbitol.</p>\n<p>d) Pellet cells once more by centrifugation (1200 x g, 5 min, 4°C, swing-out rotor) and resuspend in 2.5 mL of ice-cold 0.3M sorbitol. Pool both resuspensions in a single tube.</p>\n<p>e) Store the cell suspension on ice until needed. </p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Cell preparation",
"data_id": "0"
}
]
},
{
"id": "319300",
"is_changed": "0",
"original_id": "0",
"guid": "0B729134C6634465829EEAD65EEDBA48",
"previous_guid": "3A674EEDAB454907BEAB82DCDE053595",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p><em>This protocol was tested using the Gene Pulser Xcell electroporator (BioRad, USA) with the recommended 2 mm cuvettes (BioRad, USA).</em></p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "ElectroporatEquipment",
"data_id": "0"
}
]
},
{
"id": "319306",
"is_changed": "0",
"original_id": "0",
"guid": "4ED25CA215DA47A68682C9F63B759156",
"previous_guid": "0B729134C6634465829EEAD65EEDBA48",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>Add 3-5 μg of the linear DNA construct to a 100 μL cell suspension in a 2 mm electroporation cuvette and leave for 3-5 min at 4°C. <br /><br /><em>NB. DNA construct should include a selectable marker such as antibiotic resistance (e.g., zeocin/bleomycin)</em></p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Combining the cell suspension with desired DNA",
"data_id": "0"
}
]
},
{
"id": "319314",
"is_changed": "0",
"original_id": "0",
"guid": "1EB656469EB44888A9119D250D34DEE2",
"previous_guid": "4ED25CA215DA47A68682C9F63B759156",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>Ensure cells are resuspended in the cuvette prior to electroporation. Electroporation is performed by the following steps:</p>\n<p> </p>\n<p>a) Poring pulses (300 V, 6 pulses, 1 sec pulse Interval, 5 ms pulse length)</p>\n<p>b) Transfer pulses (40 pulses [10x4], 50 ms pulse length, 0.1 s pulse interval)</p>\n<p>c) Reverse direction of the cuvette. </p>\n<p>d) Repeat transfer pulses (40 pulses [10x4], 50 ms pulse length, 0.1 s pulse interval)</p>\n<p> </p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Electroporation",
"data_id": "0"
}
]
},
{
"id": "319387",
"is_changed": "0",
"original_id": "0",
"guid": "5DA068342E714C158A41C5433AC9EC64",
"previous_guid": "1EB656469EB44888A9119D250D34DEE2",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>Transfer the electroporated cells from the cuvette using a Pasteur pipette to 30 mL liquid growth media (without selection) and leave for 48 h under standard growth conditions</p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Cell recovery",
"data_id": "0"
}
]
},
{
"id": "319391",
"is_changed": "0",
"original_id": "0",
"guid": "4D3CD4C8434C4143A4DEFCD344132F8A",
"previous_guid": "5DA068342E714C158A41C5433AC9EC64",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>Add selection to the media and continue growth for another 48 h</p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Apply Selection",
"data_id": "0"
}
]
},
{
"id": "319398",
"is_changed": "0",
"original_id": "0",
"guid": "ECA2E8DAD3BC4EE698268C16F9FAB9C7",
"previous_guid": "4D3CD4C8434C4143A4DEFCD344132F8A",
"components": [
{
"component_type_id": "1",
"name": "Description",
"data": "<p>a) Pellet cells in 50 mL centrifuge tubes (1200 x g, 5 min, room temperature) and resuspend in 1 mL growth medium with selection.</p>\n<p>b) Spread 75 (for 7 cm diameter plates) or 250 µL (for 15 cm diameter plates) of the resuspension on growth media plates (f/2 + Si + selection, 0.9% Agar).</p>\n<p> </p>\n<p><em>Left under standard growth conditions, colonies should appear after 2-3 weeks. </em></p>",
"data_id": "0"
},
{
"component_type_id": "6",
"name": "Section",
"data": "Transfer to Solid media",
"data_id": "0"
}
]
}
],
"doi": "dx.doi.org/10.17504/protocols.io.g6nbzde",
"doi_status": "2",
"version_id": "0",
"changed_fork_steps": null,
"profile_url": "w2x234w2r2",
"protocol_img": "https://s3.amazonaws.com/pr-journal/ia2dpr6.jpg",
"profile_image": "/img/avatars/002.png",
"full_name": "Adrian Clarke",
"private_link": "87879142B7D5A76958A2335598E3456A",
"original_img": "1",
"username": "adrian-clarke",
"is_retracted": "0",
"retraction_reason": null,
"first_name": "Adrian",
"last_name": "Clarke",
"affiliation": "",
"created_by": "Adrian Clarke",
"groups": [
{
"group_id": "108",
"group_uri": "protist-research-to-optimize-tools-in-genetics-protg",
"group_name": "Protist Research to Optimize Tools in Genetics (PROT-G)",
"group_logo": "https://s3.amazonaws.com/pr-journal/e3addmn.png"
}
],
"big_protocol_img": "https://s3.amazonaws.com/pr-journal/iazdpr6.jpg",
"big_protocol_img_ofn": "skel.jpg",
"number_of_comments": 4,
"number_of_shared_runs": 0,
"tags": [],
"ownership_history": [
{
"change_time": "2017-02-10 11:52:22",
"username": "oskar-johansson",
"profile_image": "https://s3.amazonaws.com/pr-journal/icvdpr6.jpg",
"full_name": "Oskar Johansson",
"affiliation": "Biology and Environmental Sciences - Gothenburg University"
}
],
"collections": [],
"keywords": "",
"contact_badges": [],
"banner": null
}
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