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. Author manuscript; available in PMC: 2023 Sep 12.
Published in final edited form as: Cancer Cell. 2022 Aug 18;40(9):957–972.e10. doi: 10.1016/j.ccell.2022.07.012

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
rabbit anti-human DPD Abcam Cat# ab134922; Clone EPR8811
rabbit anti-human RPA2-PT21 Abcam Cat# ab61065; RRID: AB_946322
mouse anti-human RPA32/RPA2 (9H8) Abcam Cat# ab2175; RRID: AB_302873
rat-anti-cldu Abcam Cat# ab6326; RRID: AB_305426
goat anti-mouse cy 3.5 Abcam Cat# ab6946; RRID: AB_955045
goat anti-rat cy 5 Abcam Cat# ab6565; RRID: AB_955063
mouse anti-idu BD Biosciences Cat# 347580; RRID: AB_10015219
goat anti-mouse bv480 BD Biosciences Cat# 564877
rabbit anti-human pRPA32(S33) Bethyl Laboratories Cat# A300-246A; RRID: AB_2180847
mouse anti-human gH2AX (ser139)- FITC conjugated. Flow cytometry BioLegend Cat# 613404; RRID: AB_528919
rabbit anti-human p histon H2A.X (ser139). Immunofluorescence Cell Signaling Cat# 2577S
Cleaved PARP (Asp214) (D64E10) Cell Signaling Cat# 5625; RRID:AB_10699459
mouse anti-human b-actin Cell Signaling Cat# 3700; RRID:AB_2242334
Cleaved Caspase-3 Cell Signaling Cat# 9661
mouse autoanti-ssDNA DSHB Cat# N/A
horseradish peroxidase-coupled anti-rabbit GE Healthcare Cat# NA934v
horseradish peroxidase-coupled anti-mouse secondary antibody GE Healthcare Cat# NA931V
mouse anti-human p H2A.X (Ser139). Western Blotting MiliPore Cat# 05-636; RRID: AB_309864
rabbit anti-human DHODH Proteintech Cat# 14877-1-AP; RRID: AB_2091723
rabbit anti-human UCK2 Proteintech Cat# 10511-1-AP; RRID:AB_2241182
Chemicals, Peptides, and Recombinant Proteins
Urea Sigma Aldrich Cat# U5378-1kg
Complete Mini Protease Inhibitor Cocktail Roche Cat# 11836170001
Phosphatase inhibitor cocktail Roche Cat# 04906837001
Running buffer 10x Bio-Rad Cat# 1610732
4–15% Mini-PROTEAN® TGX Stain-Free™ Bio-Rad Cat# 4568085
Tween-20 VWR Cat# J640-4l
Colcemid Roche Cat# 10295892001
Accutase Sigma Aldrich Cat# A6964-100mL
Neurobasal-A Medium Invitrogen Cat# 10888-022
D-MEM/F-12 Invitrogen Cat# 11330-032
B-27 Supplement Invitrogen Cat# 12587-010
H-EGF Shenandoah Biotech Cat# 100-26
H-FGF-basic-154 Shenandoah Biotech Cat# 100-146
H-PDGF-AA Shenandoah Biotech Cat# 100-16
H-PDGF-BB Shenandoah Biotech Cat# 100-18
Heparin Stemcell Technologies Cat# 07980
Penicillin-Streptomycin (10,000 U/mL) Gibco™ Cat# 15140122
Fetal Bovine Serum Gibco™ Cat# 10437028
DMEM media Gibco™ Cat# 11995-065
HEPES (1 M) Gibco™ Cat# 15630080
Sodium Pyruvate (100 mM) Gibco™ Cat# 11360070
MEM Non-Essential Amino Acids Solution (100X) Gibco™ Cat# 11140050
GlutaMAX™ Supplement Gibco™ Cat# 35050061
Lipofectamine 2000 Life Technologies Cat# 11668-019
Polybrene santa cruz biotechnology Cat# sc-134220
CldU Sigma Aldrich Cat# C-6891
IdU Sigma Aldrich Cat# I-7125
PBS 10x GROWCELLS Cat# MRGF-6235-010Q
TBS 20x Quality Biological Inc Cat# J640-4L
Methanol (Metabolomic) Honeywell Cat #34966-6x1L
Pierce Water LC-MS Grade (Metabolomic) Honeywell Cat# 51140
TRI Reagent Sigma Aldrich Cat# 93289-100mL
Hydroxyurea Sigma-Aldrich Cat# H8627
Gimeracil Santa Cruz Biotechnology Cat# SC-207714
Merimepodib (VX-497) Selleck Chemicals Cat# S6689
5-fluorouracil (5-FU) Selleck Chemicals Cat# S1209
Gemcitabine Selleck Chemicals Cat# S1714
BAY2402234 Bayer AG N/A
OmniPur® BSA, Fraction V Sigma-Aldrich Cat# 2930-100GM
Propidium Iodide Sigma Cat# P4170
Uridine Sigma-Aldrich Cat# U30003-5g
Human TruStain FcX™ (Fc Receptor Blocking Solution) BioLegend Cat# 422301
L-Glutamine Amide-15N Cambridge Isotope Laboratories Cat# NLM-557-0.5
Hoechst 33342 Solution (20 mM) Thermo Fisher Scientific Cat# 62249
Critical Commercial Assays
SYBR Green Mix Applied Biosystems Cat #4367659
FiberPrepKit Genomic Vision Cat# EXT-001
Superscript IV Invitrogen Cat# 18090050
Cell TiterGlo Promega Cat# G7571
FITC Annexin V Apoptosis Detection Kit BioLegend Cat# 640914
FITC BrdU Flow Kit BD Biosciences Cat# 559619
Q5® High-Fidelity DNA Polymerase NEB Cat# M0491S
Deposited Data
RNA sequencing data Berlow et al., 2018, supplementary table S2 dbGaP (phs001526.v1.p1)
RNA sequencing data Zhu et al., 2021 N/A
CRISPR screen data and other data reported in this paper This paper Mendeley Data http://dx.doi.org/10.17632/yy2w57vkns.1
Experimental Models: Cell Lines
HEK293T ATCC Cat# CRL-3216
Human immortalized astrocytes (SVG p12) ATCC Cat# CRL-8621
SF8628 e Brain Tumor Research Center (BTRC) Tissue Bank N/A
BT145 The Center for Patient Derived Models N/A
BT189 The Center for Patient Derived Models N/A
BT333 The Center for Patient Derived Models N/A
BT424 The Center for Patient Derived Models N/A
BT954 The Center for Patient Derived Models N/A
BT924 The Center for Patient Derived Models N/A
BT869 The Center for Patient Derived Models N/A
SU-DIPG13 The Center for Patient Derived Models N/A
SU-DIPG17 The Center for Patient Derived Models N/A
CCHMC-DIPG1 (DIPG1) Dr. Rachid Drissi at Cincinnati Children's Hospital Medical Center N/A
CCHMC-DIPG2 (DIPG2) Dr. Rachid Drissi at Cincinnati Children's Hospital Medical Center N/A
SU-DIPG13P* Dr. Michelle Monje at Stanford University N/A
SU-DIPG4 Dr. Michelle Monje at Stanford University N/A
SU-DIPG21 Dr. Michelle Monje at Stanford University N/A
SU-DIPG33 Dr. Michelle Monje at Stanford University N/A
SU-DIPG36 Dr. Michelle Monje at Stanford University N/A
HSJD-DIPG007 Dr. Angel Montero Carcaboso at Hospital Sant Joan de Deu N/A
DIPG1-Luc This paper N/A
BT333 DPYD-Flag This paper N/A
BT954 DPYD-Flag This paper N/A
SU-DIPG4 DPYDsh1 This paper N/A
DIPG1 DPYDsh1 This paper N/A
SU-DIPG4 DPYDsh2 This paper N/A
Experimental Models: Organisms/Strains
Mice: NSG NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ The Jackson Laboratory Strain# 005557; RRID:IMSR_JAX:005557
Oligonucleotides
PCR-Forward for 18S: 5'- GAG ACT CTG GCA TGC TAA CTA G -3' Integrated DNA Technologies IDT N/A
PCR-Reverse for 18S: 5'- GGA CAT CTA AGG GCA TCA CAG -3' Integrated DNA Technologies IDT N/A
PCR-Forward for CAD: 5'-TT AGCAAGTTCCTGCGAGTC-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for CAD: 5'-CACACAGTTCTCATCCACCAT-3' Integrated DNA Technologies IDT N/A
PCR-Forward for DHODH: 5'-AAGGAAACCCTAGACCCAGA-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for DHODH: 5'-GTAACCTGTGTTCCACCACT-3' Integrated DNA Technologies IDT N/A
PCR-Forward for UMPS: 5'-CCAGAATTTCTTCACTTGACTCC-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for UMPS: 5'-TGCCACGACCTACAATGATG-3' Integrated DNA Technologies IDT N/A
PCR-Forward for UCK1: 5'-GTCAGGCTGTCTCGAAGAG-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for UCK1: 5'-TCAGAATGTCCTGGATGTGC-3' Integrated DNA Technologies IDT N/A
PCR-Forward for UCK2: 5'-GTGGATACAGATGCGGACA-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for UCK2: 5'-GCAAGCAGAATTCCTCAAAGG-3' Integrated DNA Technologies IDT N/A
PCR-Forward for UPP1: 5'-GCAGAGAAAGCTGAAAGTCAC-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for UPP1: 5'-ACACAAACTTCACATCTCCAAAC-3' Integrated DNA Technologies IDT N/A
PCR-Forward for CDA: 5'-CTGGGCATCTGTGCTGAA-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for CDA: 5'-GTGCCAAACTCTCTCATGACT-3' Integrated DNA Technologies IDT N/A
PCR-Forward for DPYD: 5'-GCACACGACTCTTGGTGAG-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for DPYD: 5'-GCAGCTCCATAATAGTTCTTGTTTG-3' Integrated DNA Technologies IDT N/A
PCR-Forward for DPYS: 5'-GCTGTGAACTGTCCTCTCTAC-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for DPYS: 5'-TCCAGTAGTGAGTGCCATCT-3' Integrated DNA Technologies IDT N/A
PCR-Forward for UPB1: 5'-TCATAGACGCATAAAGGCTATCG-3' Integrated DNA Technologies IDT N/A
PCR-Reverse for UPB1: 5'-CCCATCCTCTGCTGACTCA-3' Integrated DNA Technologies IDT N/A
Recombinant DNA
psPAX2 Addgene Cat# 12260; RRID: Addgene_12260
pMD2.G Addgene Cat# 12259; RRID: Addgene_12259
Scramble shRNA Sarbassov DD et al. Science 2005 Addgene Inc Cat# 1864
TRIPZ DPYD shRNA_1 Horizon Discovery CloneID# V2THS_84048
TRIPZ DPYD shRNA_2 Horizon Discovery CloneID# V2THS_84045
DPYD-flag Shaul YD et al., 2014 Addgene Inc. Cat# 61616;
pBABE-puro (EV plasmid) Morgenstern JP, Land H. Nucleic Acids Res. 1990 Addgene Inc Cat# 1764
CAD shRNA1 Sigma-Aldrich Cat# TRCN0000045908
CAD shRNA2 Sigma-Aldrich Cat# TRCN0000045910
DHODH shRNA1 Sigma-Aldrich Cat# TRCN0000025839
DHODH shRNA2 Sigma-Aldrich Cat# TRCN0000025868
pLenti-blasticidin-Luciferase Jean Zhao lab DFCI; Jing Ni et al. 2016 N/A
Human CRISPR Knockout Library (H3) Xu et al. Genome Res, 2015 Addgene Inc. Cat# 133914
Liu Human CRISPR Knockout Library (H1) Xu et al. Genome Res, 2015 Addgene Inc. Cat# 1000000132
Software and Algorithms
FlowJo v10.8 FlowJo LLC N/A
GraphPad Prism v9 GraphPad Software Inc. N/A
Adobe Photoshop 2021 Adobe N/A
Adobe Illustrator 2021 Adobe N/A
ImageJ NIH https://imagej.nih.gov/ij/
CellProfiler Carpenter et al., 2006 www.cellprofiler.org
Combenefit Di Veroli GY et al., 2016 https://sourceforge.net/projects/combenefit/
MAGeCK (version 0.5.9.2) Li et al., 2014 https://sourceforge.net/p/mageck/wiki/Home/
QIAGEN Ingenuity Pathway Analysis (release 2019-06-15) QIAGEN Inc. https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/
R (version 4.0.3) R Core Team (2020) https://www.r-project.org/
Fiji (version 1.0) https://eliceirilab.org/software/fiji/ https://fiji.sc/
PedCBioPortal, cBioPortal for Cancer Genomics Cerami et al., 2012 & Gao et al., 2013 https://pedcbioportal.org
BioRender BioRender Software https://biorender.com/