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/ |