REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-RAD51	McCulloch Lab (University of Glasgow)	Diagnostics Scotland (U.K)
Anti-yH2A	McCulloch Lab (University of Glasgow)	N/A
Anti-VSG2	McCulloch Lab (University of Glasgow)	N/A
Anti-VSG6	Horn Lab (University of Dundee)	Referred to here: https://doi.org/10.1073/pnas.1600344113
Anti-Myc Tag Antibody, clone 4A6	Sigma-Aldrich	Cat#05-724
Anti-EF1α Antibody, clone CBP-KK1	Sigma-Aldrich	Cat#05-235
Anti-EP Procyclic FITC Conjugate	Cederlane	Cat#CLP001F
Anti-Polymerase I	Horn Lab (University of Dundee	Referred to here: https://doi.org/10.1073/pnas.1600344113
Anti-KMX1	Hammarton Lab (University of Glasgow)	N/A
Anti-myc Alexa Fluor® 488 conjugate	Sigma-Aldrich	Cat#16-224
Alexa Fluor® 594 anti-mouse	ThermoFisher	Cat#A-11005
Alexa Fluor® 594 anti-rabbit	ThermoFisher	Cat#A-11012
Alexa Fluor® 594 anti-rat	ThermoFisher	Cat#A-11007
Alexa Fluor® 488 anti-rabbit	ThermoFisher	Cat#A27034
Alexa Fluor® 488 anti-mouse	ThermoFisher	Cat#A28175
IRDye 680RD anti-mouse	Li-Cor	Cat#926-68070
IRDye 800CW anti-rabbit	Li-Cor	Cat#926-32211
Anti-mouse HRP conjugate	ThermoFisher	Cat#62-6520
Anti-rabbit HRP conjugate	ThermoFisher	Cat#65-6120
Bacterial and Virus Strains
MAX Efficiency ™ DH5-alpha Competent Cells	ThermoFisher	Cat#18258012
DH5-alpha Competent Cells	In house prep from above	N/A
Chemicals, Peptides, and Recombinant Proteins
Methyl Methanesulfonate	Sigma-Aldrich	Cat#129925
Hydroxyurea	Sigma-Aldrich	Cat#H8627
DAPI Fluoromount-G®	Southern-Biotech	Cat#0100-20
Propidium Iodide	Sigma-Aldrich	Cat#P4170
Chameleon® Duo Pre-stained Protein ladder	Li-Cor	Cat#928-60000
HiMark Pre-stained Protein Standard	ThermoFisher	Cat#LC5699
Agencourt AMPure XP beads	Beckman Coulter	Cat#A63882
SYBR® Green PCR Master Mix	Applied Biosystems	Cat#4309155
Critical Commercial Assays
TruSeq ChIP Library Preparation Kit	Illumina	Cat#IP-202-1012
ChIP-IT® Express Enzymatic Shearing Kit	Active Motif	Cat#53035
RNeasy Mini Kit (250)	QIAGEN	Cat#74106
DNeasy Blood & Tissue Kit (250)	QIAGEN	Cat#69506
TruSeq Stranded Total RNA Kit	Illumina	Cat#20020596
Deposited Data
Sequence data is deposited in the European Nucleotide Archive	This Paper	Accession Number: PRJEB23973
Experimental Models: Cell Lines
Trypanosoma brucei: Lister 427 Bloodstream form	Laboratory of Prof Richard McCulloch	N/A
Trypanosoma brucei: TREU 927 Procyclic form	Laboratory of Prof Harry D Koning	N/A
Oligonucleotides
See Table S2 for primer details	N/A	N/A
TbRPA2 Primers FW and RV	Glover et al., 2019	https://doi.org/10.1128/mBio.01252-19
TbVEX1 Primers FW and RV	Glover et al., 2016	https://doi.org/10.1073/pnas.1600344113
Recombinant DNA
pNAT12xmyc	Alsford and Horn, 2008	https://doi.org/10.1016/j.molbiopara.2008.05.006
pGL2084 (RNAi parental plasmid: Gateway Adapted)	Jones et al., 2014	https://doi.org/10.1371/journal.ppat.1003886
Software and Algorithms
GraphPad Prism v8.	GraphPad	https://www.graphpad.com
Galaxy Server	Afgan et al., 2018	usegalaxy.org
DeepTools	Ramírez et al., 2014	https://doi.org/10.1093/nar/gkw257
FlowJo v.10	FlowJo	https://www.flowjo.com
Fiji (ImageJ)	Schindelin et al., 2012	https://doi.org/10.1038/nmeth.2019
Bowtie2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
HiSat 2	Kim et al., 2015, Pertea et al., 2016	https://ccb.jhu.edu/software/hisat2/index.shtml
RStudio		https://www.rstudio.com/
SamTools	Li et al., 2009	http://samtools.sourceforge.net
IMARIS v8.2	Oxford Instruments	https://imaris.oxinst.com
DEseq2	Love et al., 2014	https://doi.org/10.1186/s13059-014-0550-8
TopGO	Alexa et al., 2006	https://bioconductor.org/packages/release/bioc/html/topGO.html
Other
Sequence data was aligned to the T. brucei Lister 427 HGAP v.10 genome	Version 10 kindly provided by R. Cosentino	Original genome reference (v.9.) http://www.nature.com/articles/s41586-018-0619-8