Cell - 8 September 2016

STAR+METHODS

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER

Chemicals, Peptides, and Recombinant Proteins
ExoSap-It Affymetrix Cat#78201
OneTaq 2X Master Mix with Standard Buffer New England Biolabs Cat#M0482L

10XCutSmart buffer New England Biolabs Cat#B7204S
ApaLI restriction enzyme New England Biolabs Cat#R0507S

Critical Commercial Assays
Zymo YeaStar Genomic DNA kit Zymo Research Cat#D2002

BioBasic 96 yeast genomic DNA extraction kit BioBasic Cat#BS8357
Nextera TD buffer and TDE1 enzyme Illumina Cat#FC-121-1030
KAPA HiFi Library Amplification Kit KAPA Biosystems Cat#KK2612

Nextera Index kit Illumina Cat#FC-121-1012
Agencourt AMPure XP magnetic beads Beckman Coulter Cat#A63880

QIAquick PCR purification kit QIAGEN Cat#28106
Qubit HS DNA quantitation kits ThermoFisher Cat#Q-33120

Deposited Data
All Illumina sequencing data for both the whole-
genome sequencing and the fitness measurement
assays

This paper NIH BioProject: PRJNA310010

S. cerevisiae(strain S288C) reference genome, version
R64-1-1

SaccharomycesGenome

Database (SGD)

http://www.yeastgenome.org

S. cerevisiaereference genome that includes the DNA
barcode locus: sacCer3 S288C

Levy et al., 2015 NIH BioProject: PRJNA310010

Experimental Models: Organisms/Strains

S. cerevisiaeYFP-tagged ancestor strain Levy et al., 2015 GSY5306
S. cerevisiaeneutral strain with ApaLI restriction site in
barcode, used for pooled fitness assay

This paper GSY5929

Sequence-Based Reagents
Forward Primer to amplify barcode region for Sanger
sequencing (PS1): CCCGCAGAGTACTGCAATTT

This paper N/A

Reverse Primer to amplify barcode region for Sanger
sequencing (PS2): TGCACGAAAAGCAAACAAAC

This paper N/A

Primers to knock out Ras/PKA negative regulator
genes: seeSTAR Methods

This paper N/A

Primers for PCR amplification of the barcode locus:
seeSTAR Methods

This paper N/A

Software and Algorithms
TrimGalore, version 0.3.7 Felix Krueger, Babraham
Bioinformatics

http://www.bioinformatics.babraham.ac.
uk/projects/trim_galore/
Novoalign, version 3.02.02 Novocraft Technologies http://www.novocraft.com/products/novoalign/

PicardTools version 1.105(1632) Broad Institute http://broadinstitute.github.io/picard
GATK version 3.2.2 McKenna et al. (2010) N/A
Bedtools v2.17.0 Quinlan and Hall (2010) N/A

Tandem Repeat Finder Benson (1999) N/A
CLC Genomics Workbench version 8.5 QIAGEN http://www.clcbio.com
Pipeline to determine the number of barcode reads This paper https://github.com/sunthedeep/BarcodeCounter

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Cell 167 , 1585–1596.e1–e15, September 8, 2016 e1