REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Ty1 antibody (BB2), mouse	(Bastin et al., 1996)	N/A
Anti-GAP45, rabbit	(Plattner et al., 2008)	N/A
Anti-SAG2Y, rabbit	(Saeij et al., 2008)	N/A
Anti-SAG1, mouse	(Burg et al., 1988)	N/A
Anti-mouse 488	Life Technologies	Cat#A32723; RRID: AB_2633275
Anti-rabbit 594	Life Technologies	Cat#A11037; RRID: AB_2534095
Anti-mouse 594	Life Technologies	Cat#A11005; RRID: AB_2534073
Anti-mouse 647	Life Technologies	Cat#A32728; RRID: AB_2633277
Anti-CDPK1, guinea pig	Covance	Custom antibody
Anti-guinea pig IRDye 800	LICOR Biosciences	Cat#926-32411; RRID: AB_2814905
Anti-mouse IRDye 800	LICOR Biosciences	Cat#926-32210; RRID: AB_2687825
Mouse IgG Isotype Control	Thermo Fisher Scientific	Cat#14-4714-82; RRID: AB_470111
Fluorescein labeled Dolichos Biflorus Agglutinin (DBL)	Vector Laboratories	Cat#FL-1031; RRID: AB_2336394
Bacterial and Virus Strains
E. cloni electrocompetent cells	Lucigen	Cat#60117-1
NEB 5-alpha competent cells	NEB	Cat#C2987I
JM101 competent cells	Agilent	Cat#200234
Chemicals, Peptides, and Recombinant Proteins
Gentamicin	Thermo Fisher Scientific	Cat#15710072
Hoechst 33258 (CAS 23491-45-4)	Santa Cruz	Cat#sc-394049
HEPES	Sigma-Aldrich	Cat#H9897
Pyrimethamine	Sigma-Aldrich	Cat#46706-250MG
Compound 1	(Donald et al., 2002)	N/A
Mycophenolic acid	Sigma-Aldrich	Cat#M3536-50MG
Xanthine	Sigma-Aldrich	Cat#X4002-1G
6-thioxanthine	Sigma-Aldrich	Cat#T8125
TRIzol	Life Technologies	Cat#15596026
TRIzol LS	Life Technologies	Cat#10296010
Chloroform	VWR	Cat#AA22920-K2
Shield-1	Takara Bio	Cat#632189
Glycoblue	Life Technologies	Cat#AM9515
Glycogen	Life Technologies	Cat#R0561
Isopropyl-β-D-1-thiogalactopyranoside	Thermo Fisher Scientific	Cat#15529-019
chicken egg white lysozyme	Sigma-Aldrich	Cat#L3790
Imidazole	Sigma-Aldrich	Cat#I2399
PMSF Protease Inhibitor	Sigma-Aldrich	Cat#10837091001
Zwittergent 3-10 Detergent	Millipore Sigma	Cat#693021
IPTG	Thermo Fisher Scientific	Cat#15529-019
β-mercaptoethanol	Sigma-Aldrich	Cat#M6250
Magnesium sulfate heptahydrate	Sigma-Aldrich	Cat#230391
Spermidine	Sigma-Aldrich	Cat#S2626
IGEPAL CA-630	Sigma-Aldrich	Cat#I3021
PEG4000	EMD Millipore	Cat#25322-68-3
BSA	Sigma-Aldrich	Cat#A7030
RNase A	Thermo Fisher Scientific	Cat#EN0531
Prolong Diamond	Life Technologies	Cat#P36961
DNaseI	NEB	Cat#M0303L
TURBO DNA-free kit	Thermo Fisher Scientific	Cat#AM1907
BsaI	NEB	Cat#R0535L
AseI	NEB	Cat#R0526L
Exonuclease I	NEB	Cat#M0293M
Proteinase K	Life Technologies	Cat#25530-049
Phenol:Chloroform:Isoamyl solution	Invitrogen	Cat#15593031
T4 polynucleotide kinase	NEB	Cat#B0202S
T4 DNA polymerase	NEB	Cat#18005-017
Taq DNA polymerase	Thermo Fisher Scientific	Cat#EP0401
Quick ligase	Enzymatics	Cat#L6030-HC-L
iProof High-Fidelity DNA polymerase	Bio-Rad	Cat#1725301
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail tablet	Roche	Cat#11836170001
Critical Commercial Assays
QuBit dsDNA HS Assay	Life Technologies	Cat#Q32851, Cat#Q32856
DNeasy Blood and Tissue kit	QIAGEN	Cat#69506
ZR Plasmid Miniprep	Zymo Research	Cat#D4016
ZymoPURE Plasmid Maxiprep Kit	Zymo Research	Cat#D4203
Zymoclean Gel DNA Recovery Kit	Zymo Research	Cat#D4002
Nextera XT DNA Library Prep Kit	Illumina	Cat#FC-131-1024
SMARTseq v2 Low Input RNA Kit	Takara Bio	Cat#634889
MiSeq Reagent Kit V2 (50 cycles)	Illumina	Cat#MS-102-2001
NextSeq 500 V2 High Output Kit (75 cycles)	Illumina	Cat#FC-404-2005
NEBNext Ultra II Directional RNA Library Prep Kit	NEB	Cat#E7760L
TruSeq DNA Single Indexes Set A	Illumina	Cat#20015960
Q5 2x MasterMix	NEB	Cat#M0492L
KAPA HiFi PCR Mix	Kapa Biosystems	Cat#KK2602
Gibson 2x MasterMix	NEB	Cat#E2611L
Deposited Data
Next-generation sequencing data generated from genetic screens, RNA-sequencing, and CUT&RUN experiments	Gene Expression Omnibus	GEO: GSE132250
Experimental Models: Cell Lines
Human foreskin fibroblasts (HFFs)	ATCC	SCRC-1041
Experimental Models: Organisms/Strains
Toxoplasma gondii ME49 pGRA1-dsRed2.0 pBAG1-mNeonGreen pTUB1-Cas9 (bradyzoite reporter strain)	This paper	N/A
T. gondii ME49 pGRA1-dsRed2.0 pBAG1-mNeonGreen pTUB1-Cas9 BFD1-frameshift	This paper	N/A
T. gondii ME49ΔKU80 (WT)	This paper	N/A
T. gondii ME49ΔKU80ΔBFD1 (ΔBFD1)	This paper	N/A
T. gondii ME49ΔKU80ΔBFD1::BFD1WT-Ty (ΔBFD1::BFD1WT-Ty)	This paper	N/A
T. gondii ME49ΔKU80ΔBFD1::BFD1ΔMYB-Ty (ΔBFD1::BFD1ΔMYB-Ty)	This paper	N/A
T. gondii ME49ΔKU80ΔBFD1/HXGPRT::pTUB1-DD-BFD1-Ty (ΔBFD1/DD-BFD1-Ty)	This paper	N/A
Mus musculus CD-1	Charles River	Strain code: 022
M. musculus CBA/J	Jackson Labs	Strain Code: 000656
Oligonucleotides
Refer to Data S6
Recombinant DNA
Refer to Data S6
Software and Algorithms
STAR v. 2.6.1	(Dobin et al., 2013)	https://github.com/alexdobin/STAR
Bowtie2 v. 2.3.4.1	(Langmead and Salzberg, 2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Prism 8	GraphPad	https://graphpad.com
The R Project for Statistical Computing v. 3.5.0		www.r-project.org
RStudio	RStudio	Rstudio.com
DESeq2 v. 1.26	(Love et al., 2014)	https://github.com/mikelove/DESeq2
Seurat v. 2.3.4	(Butler et al., 2018)	https://github.com/satijalab/seurat
Tidyverse		https://tidyverse.tidyverse.org/
FIJI	(Schindelin et al., 2012)	https://github.com/fiji
DropSeqTools v1.0		https://github.com/broadinstitute/Drop-seq/
IGV	(Robinson et al., 2011)	http://software.broadinstitute.org/software/igv/download
FCS Express 6	De Novo Software	Denovosoftware.com
SnapGene	SnapGene	https://www.snapgene.com/
ToxoDB	(Gajria et al., 2008)	ToxoDB.org
Trim_galore v 0.4.1	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
FigTree v. 1.4.4		https://github.com/rambaut/figtree/releases
MACS2 v. 2.1.1.20160309	(Feng et al., 2012)	https://github.com/taoliu/MACS
MEME v. 4.11.4	(Bailey and Elkan, 1994)	http://meme-suite.org
Homer v. 4.10	(Heinz et al., 2010)	http://homer.ucsd.edu/homer/
BioVenn	(Hulsen et al., 2008)	http://biovenn.nl
Other
Filter holders	VWR	Cat#28163-089
Whatman Nuclepore Hydrophilic Membrane filter, 3 μm	VWR	Cat#28158-624
Whatman Nuclepore Hydrophilic Membrane filter, 5 μm	VWR	Cat#28158-704
5 μm syringe filters	Thermo Fisher Scientific	Cat#SLSV025LS
Phase lock heavy	Quantabio	Cat#2302830
Phase lock light	Quantabio	Cat#2302820
Ampure RNAClean XP bead solution	Beckman Coulter	Cat#A63987
Barcoded mRNA capture beads	Chemgenes	Cat#MACOSKO-2011-10
Ni-NTA Agarose	QIAGEN	Cat#30230
Slide-A-Lyzer Dialysis Cassettes	Thermo Fisher Scientific	Cat#66003
BioMag Plus Concanavalin A coated magnetic beads	Polysciences	Cat#86057