REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-I-A/I-E	BioLegend	Clone M5/114.15.2; RRID: AB_2565976
anti-EpCAM	BioLegend	Clone G8.8; RRID: AB_1134105
anti-H-2Db	BioLegend	Clone KH95; RRID: AB_313510
anti-CD45.2	eBioscience	Clone 104; RRID: AB_2534956
anti-H-2Kb	BD Biosciences	Clone AF6-88.5; RRID: AB_394927
Alexa Fluor 488 Phalloidin	Thermofisher	Cat# A12379; RRID: AB_2315147
Rat monoclonal anti-mCherry	Thermofisher	Clone 16D7; RRID: AB_2536611
Goat-anti-Rat polyclonal Alexa Fluor 594	Thermofisher	Cat# A-11007; RRID: AB_10561522
Critical Commercial Assays
Quick-DNA Fecal/Soil Microbe Kit	Zymo Research	Cat# D6010
anti-Cryptosporidium magnetic beads	Thermofisher	Cat# 73011
DNeasy Blood & Tissue Kit	Qiagen	Cat# 69504
Deposited Data
Raw data from WGS of Cryptosporidium tyzzeri	NCBI	SRR5683558
Assembled and annotated genome	EuPathDB	UGA55
Experimental Models: Organisms/Strains
Cryptosporidium tyzzeri	This paper	UGA55 strain
Cryptosporidium parvum	Bunchgrass Farms, ID	IOWA strain
C57BL/6 mice	Jackson Laboratory	Strain 000664
Ifng-/- mice	Jackson Laboratory	Strain 002287
Rag1-/- mice	Jackson Laboratory	Strain 002216
μMt- mice	Jackson Laboratory	Strain 002288
athymic mice	Jackson Laboratory	Strain 002019
Oligonucleotides
Primers for cloning, see Table S2	This paper	N/A
18 s probe and primer for parasite quantification, see Table S2	Jothikumar et al., 2008	N/A
Recombinant DNA
Cas9 expression vector with Cryptosporidium tyzzeri thymidine kinase locus guide	This paper and Vinayak et al., 2015	N/A
Cryptosporidium mCherry/RE9 expression cassette vector	This paper	N/A
Software and Algorithms
MEGA software package	Kumar et al., 2016	https://www.megasoftware.net/
Genome Analysis Toolkit v3.8.0	McKenna et al., 2010	https://software.broadinstitute.org/gatk/
Picard tools v2.16.0	https://broadinstitute.github.io/picard/	https://broadinstitute.github.io/picard/
Burrows-Wheeler Aligner	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
Bedtools v2.26	Quinlan and Hall, 2010	https://github.com/arq5x/bedtools2
Samtools v1.6	Li et al., 2009	http://samtools.sourceforge.net/
R with circos package	Gu et al., 2014	https://www.r-project.org/
PRISM	GraphPad	https://www.graphpad.com/scientific-software/prism/
FlowJo v10 software	TreeStar	https://www.flowjo.com/
Other
137-Cs irradiator	J.L Shepard	Mark1-30
LSRFortessa	BD Biosciences	N/A
IVIS	Caliper Life Sciences	Lumina II
ViiA 7 Real-Time System	Thermofisher	N/A