From: Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Variable | Description |
---|---|
G + C | Proportion of DNA that is guanine or cytosine |
ρt | Theoretical BD of a fragment based on fragment G + C |
ρ | BD of fragment after accounting for isotopic labeling |
σ | Standard deviation of fragment BD (ρ) |
ρmin | Minimum BD of window to be sequenced |
ρmax | Maximum BD of window to be sequenced |
ρDBLmin | Minimum BD of the DBL for a fragment |
ρDBLmin | Maximum BD of the DBL for a fragment |
A | Atom % excess of the fragment |
δ | Increase in DNA BD if atom % excess is 100% (13C: 0.036, 15N: 0.016) |
pDBL | Proportion of DNA found in the diffusive boundary layer. 1 − pDBL is the proportion of DNA found in the lumen of the tube |
pLR | Proportion of the fragment lumen population recovered in the BD window |
rt | Radius of the ultracentrifuge tube |
rmin | Minimum distance from the axis of rotation to the tube |
rmax | Maximum distance from the axis of rotation to the tube |
x | Fragment distance from the axis of rotation at equilibrium |
xmin | Minimum position on tube of the DBL range for a fragment |
xmax | Maximum position on tube of the DBL range for a fragment |
α | Abundance of the genome/fragment in the sample |
αL | Abundance of the fragment in the lumen of the tube within the BD |
αDBL | Abundance of a fragment in the DBL within the BD window |
αf | Abundance of the fragment in the BD window |
αr | Abundance of reads from the fragment |
l | Length of the fragment in base pairs |
lr | Read length in base pairs |
R | Universal gas constant (8.314 J/molK) |
T | Temperature in kelvin |
β | Proportionality constant of aqueous cesium chloride (1.14 × 109) |
G | Buoyancy factor (7.87 × 10−10) |
Mc | Mean molar weight of standard nucleotide base pair in cesium chloride solution (882) |
D | Average density of the gradient solution |
ω | Angular velocity of centrifugation |
I | Isoconcentration point |
θ | Angle of the tube relative to the axis of rotation in radians |