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. Author manuscript; available in PMC: 2022 May 10.
Published in final edited form as: Cancer Cell. 2021 Apr 8;39(5):694–707.e7. doi: 10.1016/j.ccell.2021.03.006

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
RNA Polymerase II BioLegend Cat#: 664912; RRID: AB_2650945
H3K27ac Active Motif Cat#: 39134; RRID: AB_2722569
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488 Invitrogen Cat#: A32731; RRID: AB_2633280
Chemicals, Peptides, and Recombinant Proteins
Fetal Bovine Serum Gibco Cat#: 10082147
F-12K Medium ATCC Cat#: 30-2004
DMEM/F-12, HEPES Gibco Cat#: 11330032
N-2 Supplement (100X) Gibco Cat#: 17502048
Animal-free recombinant human EGF Peprotech AF-100-15
Recombinant human FGF-basic Peprotech 100-18B
EGS (ethylene glycol bis(succinimidyl succinate)) Thermo Fisher Cat#: 21565
Formaldehyde MilliporeSigma Cat#: F8775
Glycine MilliporeSigma Cat#: G8898
AluI NEB Cat#: R0137L
BSA NEB Cat#: B9000S
dATP NEB Cat#: N0440S
Klenow (3’- 5’ exo-) NEB Cat#: M0202L
5× ligation buffer NEB Cat#: B6058S
T4 DNA ligase NEB Cat#: M0202L
ProLong™ Gold Antifade Mountant with DAPI Invitrogen Cat#: P36931
KCl Invitrogen Cat#: AM9640G
NaCl Invitrogen Cat#: AM9760G
Tris-HCl Invitrogen Cat#: 15568025
EDTA Invitrogen Cat#: AM9260G
Triton X-100 MilliporeSigma Cat#: T8787-50ML
Methanol MilliporeSigma Cat#: 34860-100ML-R
Acetic acid Thermo Fisher Cat#: A38-500
HindIII NEB Cat#: R0104M
Critical Commercial Assays
KAPA Hyper Prep Kit KAPA Biosystems Cat#: KK8505
KAPA Library Amplification Kit KAPA Biosystems Cat#: KK2612
IDT xGen Dual Index UMI Adapters IDT N/A
Lipofectamine™ 3000 Transfection Reagent Invitrogen Cat#: L3000015
Amicon Ultra-0.5 100 K column MilliporeSigma Cat#: Z740183-96EA
Chromium Genome v2 Library Kit & Gel Bead Kit 10x Genomics Cat#: PN-120258
KAPA SYBR FAST qPCR Master Mix (2X) ROX Low KAPA Biosystems Cat#: KK4620
Bionano DNA Isolation Kit Bionano Genomics Cat#: 80004
Direct Label and Stain (DLS) Labeling Kit Bionano Genomics Cat#: 80005
KAPA Stranded mRNA Sequencing Kit KAPA Biosystems Cat#: KK8502
AllPrep DNA/RNA Mini Kit QIAGEN Cat#: 80204
Deposited Data
Raw and analyzed data This paper GEO: GSE124769
WGS for PC3 ecDNA(+) Wu et al., 2019 SRA: SRR4009277
WGS for PC3 ecDNA(−) Seim et al., 2017 SRA: SRR5263237
WGS for GBM cell lines deCarvalho et al., 2018 European Genome-phenome Archive (EGA): EGAS00001001878
Experimental Models: Cell Lines
HF-2354 Ana C. deCarvalho, Henry Ford Hospital N/A
HF-2927 Ana C. deCarvalho, Henry Ford Hospital N/A
HF-3016 Ana C. deCarvalho, Henry Ford Hospital N/A
HF-3035 Ana C. deCarvalho, Henry Ford Hospital N/A
HF-3177 Ana C. deCarvalho, Henry Ford Hospital N/A
PC3 ecDNA(+) Provided by Dr. Paul Mischel lab/Ludwig Institute for Cancer Research, University of California at San Diego RRID: CVCL_0035
PC3 ecDNA(−) ATCC Cat#: CRL-1435; RRID: CVCL_0035
Oligonucleotides
See Table S4 This paper N/A
Software and Algorithms
ChIA-PET Tools Github https://github.com/cheehongsg/CPU
ChiaSigScaled Github https://github.com/cheehongsg/ChiaSigScaled
cnadjTIF Github https://github.com/WeAllOneCode/cnTIF
ChIA-DropBox Github https://github.com/TheJacksonLaboratory/ChIA-DropBox
ChIA-View Github https://github.com/TheJacksonLaboratory/ChIA-view
Long Ranger 10x Genomics https://support.10xgenomics.com/genome-exome/software/pipelines/latest/installation
Juicer Github https://github.com/aidenlab/juicer
Homer2 (v4.11.1) Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/
Cufflinks 2.2.1 Trapnell et al., 2010; Trapnell et al., 2013 https://github.com/cole-trapnell-lab/cufflinks
Trim Galore version 0.4.3 Github https://github.com/ime-tools/trimgalore
hisat 2.1.0 Kim et al., 2019 https://github.com/DaehwanKimLab/hisat2
Bionano Solve analysis software Bionano Genomics https://bionanogenomics.com/support/software-downloads/
ROSE Loven et al., 2013; Whyte et al., 2013 http://younglab.wi.mit.edu/super_enhancer_code.html
MACS2.1.0.20151222 Liu, 2014 https://pypi.org/project/MACS2/
BWA 0.7.12 Li and Durbin, 2009 https://github.com/lh3/bwa
AmpliconArchitect Deshpande et al., 2019 https://github.com/virajbdeshpande/AmpliconArchitect
readDepth Miller et al., 2011 https://github.com/chrisamiller/readdepth
Fiji (ImageJ) Open source https://fiji.sc/