add high-level metadata to assays and studies

assays/DCWMeasurement/protocols/DCWMeasurement.md

 ## DCW measurement
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 Cell dry weight measurements were carried out by transferring the cell pellet of 2 ml of cyanobacterial culture to a pre-weighed PCR tube, which was incubated at 60°C for 20 h. The tube was weighed and the difference noted as the cell dry weight, with measurements carried out in triplicates.
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assays/GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/GC-MSMeasurementsForTheQuantificationOfSqualene.md

 ## GC-MS measurements for the quantification of squalene
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 Each culture (1.5 ml) was sampled after 72 hours at the end of the growth experiment. The sample was centrifuged at 14,000 g, for five minutes and 4°C. The supernatant was discarded and the pellet was frozen at -80°C until further processing. The pellet was extracted with 500 µL acetone, containing 25 µM β-sitosterol as internal standard, under agitation at 1000 rpm and 50°C for 10 min. 500 µL of 1 M NaCl was added and mixed by vortexing. After adding 250 µL hexane, the sample was vigorously mixed for 1 min and centrifuged for phase separation (1 min at 1,780 g and 4°C). The upper hexane phase was transferred into GC-MS vials and stored at -20°C until the analysis.
 
 GC-MS analysis was carried out using a Gerstel automatic liner exchange system with multipurpose sample MPS2 dual rail and two derivatization stations, used in conjunction with a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany). For every 10-12 samples, a fresh multibaffled liner was inserted. Chromatography was performed using the Agilent 7890B GC. Metabolites were separated on an Agilent HP-5MS column (30ml x 0.25mm), the oven temperature was ramped with 12.5 °C/min from 70 °C (initial temp for 2 min) to 320 °C (final temp hold 5 min). Metabolites were ionized and fragmented in an EI source (70V, 200 °C source temp) and detected using 7200 accurate mass Q-TOF GC-MS from Agilent Technologies. Data analysis was performed using Agilent MassHunter Quantitative Analysis B.09.00. Peaks were identified using already available EI-MS fragmentation data. Peaks were identified using characteristic fragment ions (Bhatia et al., 2013) and retention times of standards (Squalene: mass/charge (m/z) = 81.07, retention time (RT) = 9.5 min; β-sitosterol: m/z = 107.09, RT = 13.6 min). Squalene concentrations in the measured samples were calculated using a calibration curve with a squalene standard (Figure S2 (SI)).
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assays/MetabolicModeling/protocols/MetabolicModelingForTheIdentificationOfAmplificationTargets.md

 ## Metabolic modeling for the identification of amplification targets
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 All simulations are based on a genome-scale stoichiometric network model of *Synechocystis* published by Knoop and colleagues (Knoop and Steuer, 2015). A modified, extended version was used, kindly provided by Ralf Steuer. All flux distributions have been calculated with constraint-based flux analysis using COBRApy (v.0.25.0) (Ebrahim et al., 2013). To simulate phototrophic growth, different constraints were applied to the model of Synechocystis (see Table S5 (SI)).
 
 FSEOF (Choi et al., 2010) was used to find amplification targets by simulating the transition from a wildtype to a production phenotype. All isoreactions were excluded for the transition experiments (Knoop and Steuer, 2015). The initial fluxes of all reactions were calculated by using the objective function to maximize the growth rate. Then, the theoretical maximum squalene production rate was calculated by setting the objective function as maximizing squalene flux. Subsequently, under constant light flux, the product formation flux rate was stepwise increased from 0% to 67% of the maximum achievable rate, while the growth rate was maximized. Only targets for which the overall mean flux rate from maximum biomass synthesis to maximum product synthesis increases were chosen. Additionally, only reactions that did not change flux direction during transition were considered. To confirm the results, flux variability analysis was performed for the selected targets, by stepwise increasing squalene flux from 0% to 67% of the maximum rate and subsequently maximizing biomass synthesis. For each simulation step, the variability of all selected targets was determined. To visualize the flux distributions a simplified network was implemented with d3flux (v.0.2.7) (St. John, 2016), a d3.js based visualization tool for COBRApy models.
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assays/PigmentQuantification/protocols/PigmentQuantification.md

 ## Pigment quantification
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 Each culture (300 µL) was sampled after 72 hours at the end of the growth experiment. The sample was centrifuged at 14,000 g for 5 minutes and 4°C. The supernatant was discarded and the pellet was resuspended in 100 μl water. The samples were frozen at -80°C until further processing. 900 μl of 100% methanol were added to the sample and the sample was mixed by vortexing. After incubation in the dark under gentle agitation for 1 h at 4°C the sample was centrifuged at 14,000 g for 5 minutes. The supernatant was transferred into a cuvette and an absorbance spectrum was measured from 400 nm to 750 nm. The absorbance spectra were divided by the OD750 or CDW and the amount of chlorophyll a in the sample was quantified by the absorbance maximum of chlorophyll a at 665 nm (A665nm) using following equation (Lichtenthaler and Buschmann 2001):
 
 *Chlorophyll content[μg/ml]=12.66 μg/ml * A665 nm*

assays/qPCR/protocols/qRT-PCR.md

 ## Quantitative real-time PCR (qRT-PCR)
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 Cultures were sampled (0.5 ml) after 72 hours at the end of the growth experiment. The pellet was processed for RNA extraction using the PGTX method (dx.doi.org/10.17504/protocols.io.jm3ck8n, Pinto et al., 2009). The remaining DNA in the extracted RNA was removed by DNase digestion using the TURBO DNA-free™ (ThermoFischer) kit according to the manufacturer’s instructions. Extracted RNAs (250 ng) were used in a reverse transcriptase reaction using the RevertAid First Strand cDNA Synthesis Kit (ThermoFischer) according to the manufacturer’s instructions. The resulting cDNA was diluted 1:20. For performing qPCR, the DyNAmo ColorFlash SYBR Green qPCR Kit was used according to the manufacturer’s instructions. Primers for sqs, dxs and the housekeeping gene rpoA are shown in Table S2 (SI). Primer efficiencies were tested before performing qRT-PCR and were deemed sufficient to yield quantitative information (Figure S3; Table S3 (SI)). Changes in gene expression as fold changes compared to the control were determined using the 2−ΔΔCT method, using rpoA as a housekeeping gene and the Δshc strain subjected to the same rhamnose concentration as a control.
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