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Each run had alternating rest/active phases, beginning with a rest phase, and consisted of 17 blocks with eight active phases (block) alternating with nine rest phases (block).
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Three-phase block diagram of pedimentation of an upland in a desert.
Genome-wide statistics were calculated on the total number of phase blocks and the N50 of individual phase block sizes in the pseudohap outputs produced in the Supernova 10x assembly.
A phased block was defined as the region spanning two markers which had a subread or linked read information providing phasing.
When switching occurred for more than two marker sites in a phased block, it was defined as a long range switch.
Haplotype phasing is still limited to the distance of individual phase blocks within scaffolds, these lengths are primarily determined based on the lengths spanning a heterozygous element such as a SNP and structural variants, so phase block lengths will differ between species as well as individuals.
In tumour cells, but not in normal cells, the S phase block has been shown to be followed by apoptosis.
Although the full genome representation is contained in the two resulting pseudohap outputs, it is phased only locally within a phase block (see Fig. 1 in the Supernova paper for an Illustration16).
For cells requiring a phase block the cells were incubated with 50 μM Nocodazole for 20 h at 37 °C per 5% CO2, counted and checked for viability using a Vi-Cell counter (Beckman Coulter, Inc., USA).
We detect an increase of cells in the G2/M phase from 20.9 to 34.3% when the cells are treated with 50 μM Nocodazole; this is consistent with the average increase of 19.0±11.0% obtained from repeating the phase block experiments with stained cells (Supplementary Fig. 3). Figure 4: Label-free prediction of DNA content for live Jurkat cells and detection of a phase blockage.
Cells were synchronized using a double thymidine block (early S-phase block).
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