KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-ATRX	Santa Cruz Biotechnology	sc-15408
anti-ATR	Santa Cruz Biotechnology	sc-51573
anti-ATRX	Bethyl Laboratories, LLC	A301-045A
anti-Vinculin	Invitrogen	#700062
anti-CHK1	Cell Signaling Technology	#2360
anti-pCHK1 Ser345	Cell Signaling Technology	#2348
anti-CHK2 pT68	Cell Signaling Technology	#2661
anti-Phospho-Histone H2A.X Ser139	Cell Signaling Technology	#2577
anti-mouse IgG, HRP-linked Antibody	Cell Signaling Technology	#7076
anti-ATM pS1981	Abcam	ab81292
HRP Goat Anti-Rabbit IgG Antibody	Vector Laboratories	P1-1000
Anti-Histone H3.3 Antibody	Millipore Sigma	#09838
Control IgG	Millipore Sigma	#12370
Alexa-Fluor 488	ThermoFisher	A-11034
Rabbit Phospho-Histone H3 (Ser10) primary antibody	Cell Signaling	3377T
Goat Anti-Rabbit IgG (H+L) FITC-conjugated secondary antibody	ThermoFisher	F2765
Chemicals, Peptides, and Recombinant Proteins
B-27 supplement	Gibco	12587-010
N-2 supplement	Gibco	17502-048
Penicillin-Streptomycin	Cellgro	30-001-CI
Normocin	Invivogen	ant-nr-1
FGF	Shenandoah Biotech	100-26
EGF	Shenandoah Biotech	100-146
GlutaMAX-I Supplement	Invitrogen	#35050061
Fetal Bovine Serum (FBS)	Sigma	F4135-500ML
Clarity™ Western ECL substrate	Bio-rad	#170-5060
DMSO	Sigma	D8418-250ML
Paraformaldehyde (PFA)	Sigma	158127-500G
Prolong™ Gold antifade reagent with DAPI	Invitrogen	P36931
AZD0156	Selleck	S8375
AZD1390	Selleck	S8680
KU-55933	Selleck	S1092
KU-60019	Selleck	S1570
Nocodazole	Sigma	M1404-10MG
Triton X-100	Sigma	T8787
Propidium Iodide	Sigma	P4864
RNase A	Qiagen	19101
Formic acid	Fisher Scientific	60-006-16
D-luciferin	Gold Biotechnology	#115144-35-9
Critical Commercial Assays
Qiagen RNeasy Mini Kit	Qiagen	#74104
TruSeq Stranded mRNA Library Kit	Illumina	#20020594
DNeasy Blood and Tissue Kit	Qiagen	#69504
Deposited Data
Raw data	this paper	GSE178116
Atrx inactivation drives disease-defining phenotypes in glioma cells of origin through global epigenomic remodeling	Danussi et al., 2018	GSE100462, GSE100464
Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma	Mackay et al., 2017	EGA - EGAS00001000226, EGAS0000100192, EGAS00001000575, EGAS00001000720, EGAS00001001139; the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/)-GSE19578, GSE26576, GSE21420, GSE34824, GSE36245, GSE36278 GSE50022, GSE50021, GSE50024, GSE55712; ArrayExpress - E-TABM-857, E-TABM-1107.
Genomic Data Commons (GDC) Data Portal	The Cancer Genome Atlas Program	https://portal.gdc.cancer.gov
single cell RNA-seq data of oligodendroglioma samples	Tirosh et al., 2016b	GSE7063
single cell RNA-seq data of astrocytomas samples	Venteicher et al., 2017	GSE89567
Experimental Models: Cell Lines
KNS42	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
SJ-GBM2	Children’s Oncology Group cell line repository	#12440053
U251 ATRXEV	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
U251 ATRXKO	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
SF188 ATRXEV	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
SF188 ATRXKO	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
UW479 ATRXEV	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
UW479 ATRXKO	Dr. Alan Meeker, Johns Hopkins University, Baltimore, MD	N/A
Human GBM D54 ATM-Luciferase inhibition reporter cells	Dr. Alnawaz Rehemtulla University of Michigan, Ann Arbor, MI	N/A
U251 ATRXKO Chk1EV	This paper	N/A
U251 ATRXKO Chk1OE	This paper	N/A
U251 ATRXKO FastFUCCI	This paper	N/A
U251 ATRXEV FastFUCCI	This paper	N/A
U251 ATRXKO Chk1EV FastFUCCI	This paper	N/A
U251 ATRXKO Chk1OE FastFUCCI	This paper	N/A
UW479 ATRXKO Chk1EV	This paper	N/A
UW479 ATRXKO Chk1KO	This paper	N/A
SF188 ATRXKO Chk1EV	This paper	N/A
SF188 ATRXKO Chk1KO	This paper	N/A
Experimental Models: Organisms/Strains
Mouse: C57BL/6	Charles River or Jackson Labs	N/A
Mouse: NOD scid gamma (NSG)	Charles River or Jackson Labs	N/A
Mouse: FVB	Charles River or Jackson Labs	N/A
Oligonucleotides
Human Chk1 Forward Primer 5′GGTGCCTATGGAGAAGTTCAA	IDT	N/A
Human Chk1 Reverse Primer 5′TCTACGGCACGCTTCATATC	IDT	N/A
Human GAPDH Forward Primer 5′GGATTTGGTCGTATTGGG	IDT	N/A
Human GAPDH Reverse Primer 5′GGAAGATGGTGATGGGATT	IDT	N/A
Primers (see Table S7)	This paper	N/A
Recombinant DNA
shp53 lentiviral plasmid	Dr. John Ohlfest, University of Minnesota, Minneapolis, Minnesota	N/A
shATRX lentiviral plasmid	generated for Koschmann et al., 2016	N/A
NRAS overexpression plasmid	Dr. John Ohlfest, University of Minnesota, Minneapolis, Minnesota	N/A
pcDNA4-Chk1-Flag Overexpression Plasmid	Addgene	#22894
pBOB-EF1-FastFUCCI-Puro Plasmid	Addgene	#86849
Software and Algorithms
chipenrich (v2.6.1)	Welch et al., 2014	https://bioconductor.org/packages/release/bioc/html/chipenrich.html
annotatr (v1.0.3)	Cavalcante and Sartor, 2017	https://www.bioconductor.org/packages/release/bioc/html/annotatr.html
Bowtie2 (v2.2.1)	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
deepTools (v.3.1.3)	Ramirez et al., 2016	https://deeptools.readthedocs.io/en/develop/
IGV (v2.11.3)	Robinson et al., 2011	https://igv.org
FastQC (v0.11.5)	Andrews, S., 2010	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
TrimGalore (v0.6.0)	Github	https://github.com/FelixKrueger/TrimGalore
STAR (v2.5.3a)	Dobin et al., 2013	https://github.com/alexdobin/STAR
HTSeq (v0.11.2)	Anders et al., 2015	https://htseq.readthedocs.io/en/master/
edgeR (v3.20.9)	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
RNA-Enrich	N/A	http://lrpath.ncibi.org
betareg	Grün et al., 2011	https://cran.r-project.org/web/packages/betareg/betareg.pdf
Seurat (v4.0.5)	Stuart et al., 2019	https://satijalab.org/seurat/
fgsea	Korotkevich et al., 2019	https://bioconductor.org/packages/release/bioc/html/fgsea.html