REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
E. coli XL-10 Gold	Strategene	Cat# 200314
Chemicals, Peptides, and Recombinant Proteins
Pentobarbital Esconarkon	Streuli Pharma	Cat# QN51AA01
Odor stimulus: bobcat urine	Main Outdoor Solutions	Cat# 91012
Odor stimulus: fox urine	Main Outdoor Solutions	Cat# 91412
Critical Commercial Assays
ACTH ELISA kit	MD Bioproducts	Cat# M046006
Corticosterone ELISA kit	Enzo Life Sciences	Cat# ADI-900-097
Mouse IL-12/IL-23 total p40 Uncoated ELISA	Invitrogen	Cat# 88-7120
Mouse IFN gamma Uncoated ELISA		Cat# 88-7314
Deposited Data
Raw fastq RNA-seq files	This paper	PRJEB32699
Experimental Models: Cell Lines
Human foreskin fibroblasts (HFFs)	ATCC	CRL-2429
Experimental Models: Organisms/Strains
Mouse: B6CBAF1/JRj	Janvier Labs	N/A
T. gondii: ME49	ATCC	506111
T. gondii: ME49Δhxgprt pBAG1-GFP	This study	N/A
T. gondii: ME49Δasp5	Hammoudi et al., 2015	N/A
T. gondii: ME49Δasp5Δhxgprt pBAG1-GFP	This study	N/A
T. gondii: ME49Δmyr1	This study	N/A
T. gondii: ME49ΔmyoJ	Frénal et al. 2017	N/A
N. caninum: Nc-Spain 7	Arranz-Solís et al., 2015	N/A
Software and Algorithms
SMART videotracking software v3.0	Panlab	Cat# 76-0695
GraphPad Prism 8	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
FASTX-Toolkit	Hannon Lab	http://hannonlab.cshl.edu/fastx_toolkit/
Trim Galore v0.4.2	Babraham Bioinformatics	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
HISAT2 v2.1.0	Kim et al., 2015	https://ccb.jhu.edu/software/hisat2/index.shtml
SAMtools v1.5	Li et al., 2009	http://samtools.sourceforge.net/
HTSeq-count v0.9.1	Anders et al., 2014	https://htseq.readthedocs.io/en/release_0.11.1/count.html
edgeR v3.24.3	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
pca3d v0.1	Weiner et al., 2012	https://cran.r-project.org/web/packages/pca3d/index.html
ggplot2 v3.1.1	Wickham, 2016	https://ggplot2.tidyverse.org/reference/index.html
gplots v3.0.1.1	Warnes, 2011	https://cran.r-project.org/web/packages/gplots/index.html
GOplot v1.0.2	Walter et al., 2015	https://wencke.github.io/
RStudio v1.1.463	R Studio Team, 2015	https://rstudio.com/
Mousemine: GeneID information, Pathway and GO enrichment analysis	Motenko et al., 2015	http://www.mousemine.org/mousemine/begin.do
Amira v 2019.1	Thermo Fisher Scientific	https://www.fei.com/software/amira/
Imaris v 9.3.0	Oxford Intruments	https://imaris.oxinst.com/
Other
X-CLARITY protocol	Chung lab	http://www.chunglabresources.com/cl1#cl-protocol
mesoSPIM Initiative		http://mesoSPIM.org