arc init

assays/SugarMeasurement/dataset/sugar_result.csv

+MeasuredSugar,RT_M1,RT_M2,RT_M3,Cold_M1,Cold_M2,Cold_M3
+Glucose,27.671,24.881,22.634,24.665,32.118,29.067
+Fructose,9.283,7.913,7.945,8.752,9.679,9.671
+Sucrose,9.294,7.272,8.236,7.612,9.495,9.344
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assays/SugarMeasurement/protocols/sugar_extraction_protocol.md

+
+# Sugar/Starch Extraction
+
+* Grind samples in liquid nitrogen and weigh out 20 to a maximum of 100 mg. (Note the weighed amount?!)
+* Add 500µl of water to, for example, 50 mg of sample and place it directly in a thermoblock at 95°C for 15 minutes. After 10 minutes, vortex each sample for 3-4 seconds. [Place samples in the thermoblock at regular intervals to ensure all samples are treated equally and remain in the thermoblock for 15 minutes.]
+* After 15 minutes, vortex the samples well and let them cool to room temperature (RT).
+* Centrifuge for 10 minutes at 20,000g, 40°C.
+* Transfer the supernatant to a new tube and store at -20°C for sugar measurement (samples for sugar measurement are now ready).
+* Add 500µl of ethanol (80% abs.) to the pellet and resuspend.
+* Centrifuge for 10 minutes at 20,000g, 4°C.
+* Discard the supernatant.
+* Add 500µl of ethanol (80% abs.) to the pellet and resuspend.
+* Centrifuge for 10 minutes at 20,000g, 4°C.
+* Discard the supernatant.
+* Add 500µl of autoclaved water to the pellet and resuspend.
+* Centrifuge for 10 minutes at 20,000g, 4°C.
+* Discard the supernatant.
+* Depending on the initial weighed amount, add 250µl of freshly prepared sodium acetate (50mmol, pH 4.7).
+* Autoclave for 20 minutes, liquid program (Program 8).
+
+Set up starch digestion overnight with shaking at 37°C:
+For 100 samples: 100 x 250µl NaAc (50 mM) = 25ml total volume.
+25mg α-Amylase (SIGMA; 9000-90-2) [final concentration: 1mg/ml], or 5 units per sample.
+1125µl Amyloglucosidase (ROCHE from Asp. Niger; 10102857001) [final concentration: 45µl/ml], or 5 units per sample.
+
+## The next day
+
+- Place all samples in a thermoblock for 10 minutes at 95°C to inactivate the enzymes.
+- Centrifuge for 10 minutes at 20,000g (For the calculation, add the volume of x µl added before autoclaving and the 250 µl enzyme mix).
+
+### Premix for Sugar/Starch Measurement (100 samples)
+
+- 10ml water
+- 6ml HEPES (stock: 333mM, pH 7.5, autoclaved)
+- 1ml MgCl2 (stock: 200mM, sterile filtered)
+- 1ml ATP (stock: 40 mM, aliquoted and stored at -20°C)
+- 1ml NADP (stock: 16mM, aliquoted and stored at -20°C)
+- 10µl Glu-6-P-DH (from Leuconstock)
+
+### For each sample measurement
+
+* Pipette 190µl premix and 10µl sample into a well (96-well plate).
+Program: Desktop > Olli-Starch: Start. The program runs 5 cycles [blank later].
+* The program will automatically eject the plate to add hexokinase/PGI/invertase (from the refrigerator: diluted 1:10 in HEPES; add 1µl using a stamping plate).
+* Insert the plate.
+* The measurement resumes: When the values begin to stabilize, the measurement can be stopped.
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studies/AthalianaColdStress/protocols/growth_protocol.md

+# Study Name: Growth Protocol for *Arabidopsis thaliana*
+
+## Parameters:
+- 200 µmol photons m²/s (200 Einstein)
+- Alternating 6°C (cold treatment) and 25°C (control)
+- 4 days
+
+## Characteristics:
+- *Arabidopsis thaliana*
+- Leaf
+- Hydroponic culture
+- Columbia (Col-0)
+
+### Protocol Overview:
+1. **Preparation of Hydroponic System**:
+   - Prepare nutrient solution suitable for *Arabidopsis* growth.
+   - Set up hydroponic culture system with proper aeration and nutrient circulation.
+
+2. **Seed Germination and Transfer**:
+   - Germinate *Arabidopsis thaliana* seeds (Columbia ecotype) in nutrient agar plates.
+   - After 7-10 days of germination, transfer seedlings into hydroponic culture trays.
+
+3. **Growth Conditions**:
+   - For cold stress treatment, expose plants to 6°C under continuous light at 200 µmol photons m²/s for the 4-day growing period.
+   - For control plants, maintain at 25°C under the same light intensity for the same duration.
+
+4. **Monitoring and Sampling**:
+   - Monitor leaf development and sample at regular intervals to assess the impact of cold temperature on leaf physiology and growth.
+
+5. **End of Experiment**:
+   - After 4 days, collect leaf samples for further analysis of physiological and molecular responses.
+
+This protocol ensures that temperature and light conditions are strictly controlled to study the cold response in *Arabidopsis thaliana*.
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