Additional file 1 of A high-throughput microfluidic diploid yeast long-term culturing (DYLC) chip capable of bud reorientation and concerted daughter dissection for replicative lifespan determination
Creators: name: Wang, Yingying
name: Zhu, Zhen
name: Liu, Ke
name: Xiao, Qin
name: Geng, Yangye
name: Xu, Feng
name: Ouyang, Shuiping
name: Zheng, Ke
name: Fan, Yimin
name: Jin, Nan
name: Zhao, Xiangwei
name: Marchisio, Mario A.
name: Pan, Dejing
name: Huang, Qing-an
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Figure S1. CFD simulation of hydrodynamic forces exerted on an immobilized budding yeast cell. (A) Hydrodynamic forces on the bud quantified by arrow length during hydrodynamic rotation of budding yeast from upstream to downstream in a 45-degree interval on the xz plane. (B) Hydrodynamic forces on a growing bud (diameter: 2 μm, 3 μm and 4 μm) towards the downstream to evaluate the cell retention and daughter detachment in the orifice. Figure S2 Calculation of RLS and BTI by using the digital matrix and oscillogram recorded from the representative cell in Figure 5(A). Figure S3 Wireframes of the model geometry containing channel walls (black), a 5 × 5 array of cell traps (blue) and immobilized yeast cells (brown) and culturing medium filled in the residual space of the model. (A) 3D view of the simplified geometric model established as follows: A 5 × 5 cell-trap array with different settings of geometric features (dr and dm) was placed in the middle of a microchannel, which featured 400 μm × 8 μm outer profile in xz-dimension and variable length dy in y-axis for fitting 5 columns of traps. The distance between adjacent columns was set to 30 μm. (B) 2D cross-section view of the array for particle trajectory tracing. dr, dm and dy in modeling were set to 34 μm, 17 μm and 158 μm, respectively. Figure S4. 3D wireframe of the model geometry in simulation of bud rotation in a single trap, containing channel walls (black), a trap (blue) and a budding yeast cell (brown) and culturing medium filled in the residual space of the model. Geometric conditions were set as follows: The trap was placed in the center with 30 μm × 34 μm × 8 μm outer profile in xyz-dimension; the budding yeast cell was set as a conjugation of an ellipsoid (5 μm × 4.4 μm) and a sphere (2 μm in diameter), contacting with each other at the upstream end of the major axis of the ellipsoid initially. To imitate the bud rotation in the trap, the mother cell together with its bud, were set to rotate from -x to +x direction along the xz-plane with a 45-degree interval, meanwhile the mother was kept contacting with the “bowl” bottom; to imitate bud growth after the bud was relocated in the narrow orifice, the diameter of the sphere was set 2 μm, 3 μm and 4 μm, respectively. Table S1. A comparison of reported RLS data of budding yeast using conventional and microfluidic methods. Table S2. Geometric settings of the cell-trap array in CFD simulation. Table S3. General settings and parameters in CFD simulation. Table S4. Settings and parameters of particle trajectory tracing in cell-trapping simulation