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Colony-forming efficiency was calculated, cell cycle and apoptosis were measured, and changes in cell cycle- and apoptosis-related gene expression were measured by microarray.
Cell proliferation was measured by CCK-8, colony-forming efficiency was calculated, cell cycle and apoptosis were measured, and changes in cell cycle- and apoptosis-related gene expression were measured by Western blotting.
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To calculate cell cycle and S phase duration, HH10 embryos were exposed to EdU for defined periods (1 or 4 h), fixed and processed to detect EdU-labelled DNA using Click-iT EdU kit (Molecular Probes) following manufacturer's instructions.
We calculated the cell cycle periodicity index CCP [51] of each of these genes from the expression data, and searched their promoter sequences, from +200 to −1000 bp from the TSS, for every one of the 5 motifs.
We then calculated the cell cycle phase of the imaged cells by measuring their DNA content using diamidino-2-phenylindole (DAPI) seeining (see Methods section for details).
In addition, on two occasions when we observed a second round of division of one of the daughter pair, we were able to calculate the cell cycle time to be 510 and 600 minutes.
Authors of the first paper [ 27], used the Fucci system (the first marker indicates G0/G1 phases, and the second one the S/G2/M phases) to calculate length of cell cycle and cell cycle phases.
DNA histograms were analysed using FlowJo v10 software and the percentage of cells in the G0/G1, S, and G2/M phase of the cell cycle calculated (n = 3 ± SD).
Potency reflects the fixed points of the network under a given environmental condition and reprogramming perturbation, and all initial states are considered when calculating the percentage of cell cycle attractors.
The distribution of cells in each phase of the cell cycle was calculated using ModFit software.
The relative distribution of cells in the phases of the cell cycle was calculated with ModFiLT software (Becton Dickinson).
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