Cell - 8 September 2016
and the frequent polyploidization events in the evolutionary his- tory of many organisms, includingS. cerevisiae(Marcet-Houben a ...
Center for Computational, Human and Evolutionary Genomics (CEHG); E.E. by NSF GFRP DGE-1247312; J.C. by NSF GRFP DGE-114747; A.A ...
Oleksyk, T.K., Smith, M.W., and O’Brien, S.J. (2010). Genome-wide scans for footprints of natural selection. Philos. Trans. R. S ...
STAR+METHODS KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins ExoSap-It A ...
CONTACT FOR REAGENT AND RESOURCE SHARING Further information regarding the manuscript may be directed to the lead contact Dmitri ...
the frequencies of the clones at five time points by Illumina amplicon sequencing of their DNA barcodes. The frequencies from fo ...
Optimizing Sequencing Costs We determined that we neededz1 million reads per time point for Illumina amplicon sequencing of the ...
beginning the assay as before. This second 48 hr growth was done to accustom the cells to the medium and to minimize the freezer ...
For the first cycle, for each sample, we performed 12 PCR reactions. Master Mix: d 325 ml OneTaq 2x master mix (NEB # M0482L) d ...
Multiplexing and Amplicon Sequencing We used Qubit HS kits (ThermoFisher # Q-33120) to quantify the concentration of our size-se ...
After building an index for the bam file with PicardTools, we then got global coverage metrics with GATK version 3.2.2 (McKenna ...
After structural variant calling was completed, we filtered out structural variants that occurred in previously known repetitive ...
Introduction to Fitness Estimation Methodology The fitness of a barcoded lineage relative to the rest of the population determin ...
Varðri+ 1 Þzkihri+ 1 i (7) wherekiis a parameter fit from the data for many barcode families. For nearly neutral lineages, there ...
Whilekiincreases with increasing coverage ratio, the variance in the fitness estimate decreases with increasing read depth. For ...
We carried out the following procedure using the1500 lineages which were neutral in the experiments ofLevy et al. (2015) dEstim ...
The multiplicative noise varies little across time points and experiments, typically10%/cycle corresponding to uncertainties in ...
Within each batch we tested the hypothesis that the means of the fitness distributions for different classes were different. We ...
Supplemental Figures Figure S1. Estimated Barcoded Fraction of Populations during Pooled Fitness Measurement, Related toFigure 2 ...
Figure S2. Noise Analysis for Batch 1, Related toFigure 2 The first two rows of panels show histograms of scaled deviations Zifo ...
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