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scinote-web/app/assets/templates/experiment_1/experiment.json
Andrej 230aea15fc Update experiment templates [SCI-7314]
2022-10-11 15:55:56 +02:00

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{
"experiment": {
"id": 1,
"name": "Polymerase chain reaction",
"description": "Polymerase chain reaction (PCR) monitors the amplification of DNA in real time (qPCR cyclers constantly scan qPCR plates). It is, in contrast to the conventional PCR, quantitative, meaning that it enables us to determine the exact concentration (relative or absolute) of the amplified DNA in the sample. Conversely, in conventional PCR we can see the result of amplification only after the PCR is completed (end-point detection).\n\n Apart from DNA, RNA can also be used as a template (e.g. in case of gene expression studies or detection of RNA viruses). In this case, the RNA needs to be reverse transcribed into DNA (also termed complementary DNA or cDNA) before it is amplified with real-time PCR. There is a term for this combined method: real-time reverse transcription PCR or qRT-PCR (sometimes RT-qPCR) for short.",
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"uuid": "0bfd6305-8ede-46d9-9d53-df6d6c6c22ec"
},
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],
"step_orderable_elements": [
{
"step_text": {
"text": "Compare response of PVYNTN, cab4 and PR1 genes in mock/virus inoculated potatoes & in time"
},
"position": 0
},
{
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"id": 1,
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},
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}
],
"step_orderable_elements": [
{
"step_text": {
"text": "50% of samples should be mock inoculated and the other 50% should be inoculated with the PVY NTN virus."
},
"position": 0
},
{
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"name": "Table 1",
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},
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"step_orderable_elements": [
{
"step_text": {
"text": "50% of PVY NTN inoculated potatoes and 50% of mock inoculated potatoes collect 1 day post inoculation, while the other half of the samples collect 6 days post inoculation."
},
"position": 0
}
]
},
{
"step": {
"id": 3,
"name": "Store samples",
"position": 1,
"completed": false,
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"created_at": "2020-12-19T18:26:29.177Z",
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},
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],
"step_orderable_elements": [
{
"step_text": {
"text": "Collect samples in <strong>2ml tubes</strong> and put them in <strong>liquid nitrogen</strong> or store at <strong>-80°C</strong>."
},
"position": 0
}
]
}
]
}
],
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]
},
{
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"name": "RNA isolation",
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}
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"step": {
"id": 16,
"name": "If the expected RNA yield is >30 μg",
"position": 11,
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"created_at": "2020-12-21T09:20:11.351Z",
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"step_text": {
"text": "<html><body><p>If the expected RNA yield is &gt;30 μg, repeat Step 9 using another 30–50 μL of RNase-free water.<br>Alternatively, use the eluate from Step 9 (if high RNA concentration is required). Reuse the collection tube from Step 12.</p></body></html>"
},
"position": 0
}
]
},
{
"step": {
"id": 15,
"name": "Place the RNeasy spin column in a new 1.5 ml collection tube",
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"step_text": {
"text": "Add 30–50 μL RNase-free water directly to the spin column membrane. Close the lid, and centrifuge for 1 min at ≥8000 x g to elute the RNA."
},
"position": 0
}
]
},
{
"step": {
"id": 14,
"name": "Addition of buffer",
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"completed": false,
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},
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"step_orderable_elements": [
{
"step_text": {
"text": "Add 500 μL Buffer RPE to the RNeasy spin column. Close the lid, and centrifuge for 2 min at ≥8000 x g."
},
"position": 0
}
]
},
{
"step": {
"id": 13,
"name": "Add 700 μL Buffer RW1 to the RNeasy spin column.",
"position": 8,
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"created_at": "2020-12-21T06:12:38.398Z",
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},
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"step_orderable_elements": [
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"step_text": {
"text": "Close the lid, and centrifuge for 15 s at ≥8000 x g. Discard the flow-through."
},
"position": 0
}
]
},
{
"step": {
"id": 12,
"name": "Transfer the sample",
"position": 7,
"completed": false,
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},
"step_comments": [
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],
"step_orderable_elements": [
{
"step_text": {
"text": "Transfer the sample (usually 650 μl), with any precipitate, to an RNeasy Mini spin column (pink) in a 2 mL collection tube (supplied). Close the lid, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flowthrough."
},
"position": 0
}
]
},
{
"step": {
"id": 11,
"name": "Addition of ethanol",
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"completed": false,
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"created_at": "2020-12-21T08:54:08.994Z",
"updated_at": "2020-12-21T15:54:04.636Z",
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},
"step_comments": [
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],
"step_orderable_elements": [
{
"step_text": {
"text": "Add 0.5 volume of ethanol (96–100%) to the cleared lysate, and mix immediately by pipetting. Do not centrifuge."
},
"position": 0
}
]
},
{
"step": {
"id": 10,
"name": "Transfer the lysate to a QIAshredder spin column",
"position": 5,
"completed": false,
"completed_on": null,
"user_id": 1,
"created_at": "2020-12-21T09:50:20.299Z",
"updated_at": "2020-12-21T15:54:04.631Z",
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"assets_view_mode": "thumbnail"
},
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"step_orderable_elements": [
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"step_text": {
"text": "Transfer the lysate to a QIAshredder spin column placed in a 2 mL collection tube. Centrifuge for 2 min at full speed. Transfer the supernatant of the flow-through to a new microcentrifuge tube (not supplied) without disturbing the cell-debris pellet."
},
"position": 0
}
]
},
{
"step": {
"id": 9,
"name": "Buffer addition",
"position": 4,
"completed": false,
"completed_on": null,
"user_id": 1,
"created_at": "2020-12-21T09:10:51.182Z",
"updated_at": "2020-12-21T15:54:04.627Z",
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"assets_view_mode": "thumbnail"
},
"step_comments": [
],
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],
"step_orderable_elements": [
{
"step_text": {
"text": "Add 450 μL Buffer RLT or Buffer RLC to a maximum of 100 mg tissue powder. Vortex vigorously."
},
"position": 0
}
]
},
{
"step": {
"id": 8,
"name": "Disruption",
"position": 3,
"completed": false,
"completed_on": null,
"user_id": 1,
"created_at": "2020-12-21T07:50:13.585Z",
"updated_at": "2020-12-21T15:54:04.620Z",
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},
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"step_text": {
"text": "<html><body><p>Disruption using the TissueLyser II, TissueLyser LT, or TissueRuptor.<br><br>For detailed information on disruption of plant tissues for purification of RNA, see TissueLyser Handbook, TissueLyser LT Handbook, or TissueRuptor Handbook. (The RNeasy Mini Handbook will be updated with this option.)</p></body></html>"
},
"position": 0
}
]
},
{
"step": {
"id": 7,
"name": "Disruption with mortar and pestle",
"position": 2,
"completed": false,
"completed_on": null,
"user_id": 1,
"created_at": "2020-12-21T07:46:29.882Z",
"updated_at": "2020-12-21T15:54:04.612Z",
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},
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"step_orderable_elements": [
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"step_text": {
"text": "Immediately place tissue in liquid nitrogen. Grind thoroughly. Decant tissue powder and liquid nitrogen into RNase-free, liquid-nitrogen–cooled, 2 mL microcentrifuge tube (not supplied). Allow the liquid nitrogen to evaporate, but do not allow the tissue to thaw. Proceed immediately to step 5."
},
"position": 0
}
]
},
{
"step": {
"id": 6,
"name": "Isolation of RNA with RNeasy plant mini kit",
"position": 1,
"completed": false,
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"created_at": "2020-12-21T09:24:02.300Z",
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"step_text": {
"text": "Disrupt a maximum of 100 mg plant material according to step 3 or 4."
},
"position": 0
}
]
},
{
"step": {
"id": 5,
"name": "Homogenization of the material",
"position": 0,
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"created_at": "2020-12-21T06:34:41.820Z",
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},
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"step_text": {
"text": "Use tissue lyser: 1 min on step 3."
},
"position": 0
}
]
}
]
}
],
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]
},
{
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"text": "For optimal results, stabilize harvested tissues immediately in RNAlater RNA Stabilization Reagent (see protocol on page 34). Tissues can be stored in the reagent for up to 1 day at 37°C, 7 days at 15–25°C, or 4 weeks at 2–8°C, or archived at –20°C or –80°C.",
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"text": "β-Mercaptoethanol (β-ME) must be added to Buffer RLT before use. Add 10 µl β-ME per 1 mL Buffer RLT. Dispense in a fume hood and wear appropriate protective clothing. Buffer RLT containing β-ME can be stored at room temperature (15–25°C) for up to 1 month. Alternatively, add 20 µL of 2 M dithiothreitol (DTT) per 1 mL Buffer RLT. The stock solution of 2 M DTT in water should be prepared fresh or frozen in single-use aliquots. Buffer RLT containing DTT can be stored at room temperature for up to 1 month.",
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