REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat Anti-Rat IgG (H+L), Alexa Fluor 594 Conjugated	Thermo Fisher	Cat#A-11007; RRID: AB_141374
Rabbit Anti-Mouse IgG (H+L), Alexa Fluor488 Conjugated	Thermo Fisher	Cat#A-11059; RRID: AB_142495
Goat Anti-Rabbit IgG (H+L), Alexa Fluor488 Conjugated	Thermo Fisher	Cat#A-11034; RRID: AB_2576217
Goat Anti-Mouse IgG (H+L), Alexa Fluor594 Conjugated	Thermo Fisher	Cat#A-11005; RRID: AB_2534073
Goat Anti-Rabbit IgG (H+L), Alexa Fluor594 Conjugated	Thermo Fisher	Cat#A-11037; RRID: AB_2534095
Rabbit anti-53BP1	Bethyl Laboratories	Cat#A300-272A; RRID: AB_185520
Mouse monoclonal anti-γH2AX, clone JBW301	Millipore	Cat#05-63; RRID: AB_309864
Mouse monoclonal anti-RPA32/RPA2	Abcam	Cat#ab2175; RRID: AB_302873
Rabbit anti-Phospho-ATR (Ser428)	Cell Signaling Technology	Cat#2853; RRID: AB_2290281
Rabbit anti-RTEL1	Novus Biologicals	Cat#NBP2-22360; RRID: AB_2722642
Rabbit anti-PCNA	Santa Cruz	Cat#SC7907; RRID: AB_2160375
Mouse anti-PCNA	Santa Cruz	Cat#SC56; RRID: AB_628110
Rabbit anti-TRF2	Cell Signaling Technology	Cat#13136; RRID: AB_2722641
Rabbit anti-V5	Sigma-Aldrich	Cat#V8137; RRID: AB_261889
Rabbit anti-GFP	Abcam	Cat#ab290; RRID: AB_303395
Mouse anti-GFP	Roche	Cat#11814460001; RRID: AB_390913
Mouse anti-RNA polymerase II CTD repeat YSPTSPS	Abcam	Cat#ab817; RRID: AB_306327
Rat monoclonal anti-BrdU	Abcam	Cat#ab6326; RRID: AB_305426
Mouse monoclonal anti-BrdU	Becton Dickinson	Cat#347580; RRID: AB_10015219
Mouse anti-GAPDH	Abcam	Cat#ab8245; RRID: AB_2107448
Mouse anti-TUBULIN	Sigma-Aldrich	Cat#T6074; RRID: AB_477582
Mouse anti-S9.6	The Francis Crick Institute Cell Services	RRID: AB_2313773
Chemicals, Peptides, and Recombinant Proteins
Adenovirus Ad-Cre-GFP	Vector Biolabs	Cat#1700
Adenovirus Ad-GFP	Vector Biolabs	Cat#1060
Adenovirus Ad-iCre-RFP	Vector Biolabs	Cat#1774
Adenovirus Ad-RFP	Vector Biolabs	Cat#1660
CldU	Sigma-Aldrich	Cat#C6891
IdU	Sigma-Aldrich	Cat#I7125
TMPyP4	Millipore	Cat#613560
Hydroxytamoxifen	Sigma-Aldrich	Cat#H7904
Doxycycline	Sigma-Aldrich	Cat#D9891
Geneticin G418 sulfate	GIBCO	Cat#11811-031
Propidium Iodide	Sigma	Cat#P4864
TelC PNA probe	PANAGENE	Cat#F2003
Proteinase K recombinant	Roche	Cat#40278100
Lipofectamine 2000	Thermo Fisher	Cat#11668027
Fluoroshield with DAPI	Sigma-Aldrich	Cat#F6057
Critical Commercial Assays
RNeasy Mini Kit	QIAGEN	Cat#74106
QIAprep Spin Miniprep Kit	QIAGEN	Cat#27106
Duolink® In Situ PLA® Probe Anti-Rabbit MINUS	Sigma-Aldrich	Cat# DUO92005
Duolink® In Situ PLA® Probe Anti-Mouse PLUS	Sigma-Aldrich	Cat# DUO92001
Duolink® In Situ Detection Reagents Red	Sigma-Aldrich	Cat# DUO92008
Duolink® In Situ Wash Buffers, Fluorescence	Sigma-Aldrich	Cat# DUO82049
Deposited Data
Original, unprocessed data	This study	https://doi.org/10.17632/w8zh77nk36.1
Sequencing	This study	GEO: GSE161597
Experimental Models: Cell Lines
Mouse Embryonic Fibroblasts Rtel1F/F	Vannier et al., 2012	N/A
Mouse Embryonic Fibroblasts TamCre Rtel1F/F	This study	N/A
Mouse Embryonic Fibroblasts Rtel1F/F;pBabe Rtel1C1252A/C1255A	Sarek et al., 2015	N/A
Mouse Embryonic Fibroblasts Terf1F/F	This study	N/A
Mouse Embryonic Fibroblasts Rtel1F/F;WT RNaseH1GFP	This study	N/A
Mouse Embryonic Fibroblasts Rtel1F/F;D210N-RNaseH1GFP	This study	N/A
Mouse Embryonic Fibroblasts Rtel1+/+-V5;WT RNaseH1GFP	This study	N/A
Mouse Embryonic Fibroblasts Rtel1IA/IA-V5;WT-RNaseH1GFP	This study	N/A
Mouse Embryonic Fibroblasts Rtel1F/F;pBabe Rtel1C1252A/C1255A ; D210N RNH1-GFP	This study	N/A
Software and Algorithms
Adobe Photoshop CC	Adobe	https://www.adobe.com/es/products/photoshop.html
ImageJ	NIH	https://imagej.nih.gov/ij/
Volocity 6.3	PerkinElmer	https://www.perkinelmer.com/uk/lab-products-and-services/resources/cellular-imaging-software-downloads.html
GraphPad Prism 7	GraphPad	https://www.graphpad.com/
Flow Jo 10	FlowJo	https://www.flowjo.com/
FastQC	Daley and Smith, 2013	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
nf-core/chipseq	Ewels et al., 2020	https://zenodo.org/record/3966161
picard-tools	Broad Institute	http://broadinstitute.github.io/picard
Pysam	GitHub	https://github.com/pysam-developers/pysam
ggplot2	(Wickham et al., 2016)	https://ggplot2-book.org/
cutadapt	(Martin, 2011)	https://journal.embnet.org/index.php/embnetjournal/article/view/200
Fgsea	(Korotkevich et al., 2019)	https://www.biorxiv.org/content/10.1101/060012v2.full
Trim Galore!	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Nextflow	Tommaso et al., 2017	https://nextflow.io/
Singularity	Kurtzer et al., 2017	https://sylabs.io/guides/2.6/user-guide/quick_start.html
Burrows-Wheeler Alignment tool	Li and Durbin, 2009	http://maq.sourceforge.net
SAMtools	Li et al., 2009	http://samtools.sourceforge.net
BEDTools	Quinlan and Hall, 2010	https://code.google.com/archive/p/bedtools
BamTools	Barnett et al., 2011	https://github.com/pezmaster31/bamtools
bedGraphToBigWig	Kent et al., 2010	http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
MACS2	Zhang et al., 2008	https://github.com/macs3-project/MACS
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/
featureCounts	Liao et al., 2014	http://subread.sourceforge.net
R	R core team	https://www.r-project.org/
DESeq2	Love et al., 2014	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
MultiQC	Ewels et al., 2016	https://multiqc.info/
deepTools	Ramirez et al., 2016	https://deeptools.readthedocs.io/
phantompeakqualtools	Landt et al., 2012	http://www.modencode.org/; https://www.encodeproject.org/
RSEM	Li and Dewey, 2011	http://deweylab.biostat.wisc.edu/rsem
STAR	Dobin et al., 2013	https://code.google.com/archive/p/rna-star
UCSC Table Browser	Karolchik et al., 2004	http://genome.ucsc.edu/
IGV genome browser	Robinson et al., 2011	https://www.broadinstitute.org/igv/
UpSetR	Conway et al., 2017	https://github.com/hms-dbmi/UpSetR/
G4Hunter	Bedrat et al., 2016	http://bioinformatics.ibp.cz.
ChIPseeker	Yu et al., 2015	http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html
BioMart	Smedley et al., 2009	http://www.biomart.org
Custom scripts	This study	https://github.com/arpoe/KotsantisP_CellReps_2020