KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Antibodies | |||
| Anti-beta Tubulin antibody – Loading Control | Abcam | Cat#ab6046; RRID: AB_2210370 | |
| Anti-Cas9 Antibody (7A9–3A3) | Santa Cruz Biotechnology | Cat#sc-517386; RRID: AB_2800509 | |
| Donkey anti-rabbit IgG, Whole Ab, HRP-conjugated | GE Healthcare | Cat#NA934, RRID: AB_772206 | |
| Donkey anti-Mouse IgG (H+L), HRP-conjugated | Thermo Fisher Scientific | Cat#PA1–28748, RRID: AB_10982166 | |
| Bacterial and virus strains | |||
| Subcloning Efficiency DH5alpha Competent Cells | Invitrogen | Cat#18265017 | |
| Chemicals, peptides, and recombinant proteins | |||
| FuGENE 6 | Promega | Cat#E2691 | |
| Collagenase/Hyaluronidase | Stemcell Technologies | Cat#07912 | |
| Gentle Collagenase/Hyaluronidase | Stemcell Technologies | Cat#07919 | |
| Hydrocortisone | Stemcell Technologies | Cat#74144 | |
| Dispase | Stemcell Technologies | Cat#07923 | |
| DNase I | Stemcell Technologies | Cat#07900 | |
| Blasticidin | Corning | Cat#30100RB | |
| Lenti-X Concentrator | Takara | Cat#631231 | |
| Polybrene | Millipore | Cat#TR1003G | |
| RNAiMAX | Invitrogen | Cat#13778075 | |
| Critical commercial assays | |||
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 | 10x Genomics | Cat#PN-1000075 | |
| Chromium Single Cell ATAC Library & Gel Bead Kit v1 | 10x Genomics | Cat#PN-1000110 | |
| Chromium Chip B Single Cell Kit | 10x Genomics | Cat#PN-10000153 | |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat#PN-120262 | |
| Chromium Chip E Single Cell ATAC Kit | 10x Genomics | Cat#PN-1000082 | |
| Chromium i7 Multiplex Kit N, Set A | 10x Genomics | Cat#PN-1000084 | |
| Quick-RNA Miniprep Kit | Zymo | Cat#R1055 | |
| Turbo DNA-free Kit | Invitrogen | Cat#AM1907 | |
| iScript cDNA Synthesis Kit | BioRad | Cat#1708891 | |
| Deposited data | |||
| scRNA-seq (processed data) | This Paper | GSE173682 | |
| scATAC-seq (processed data) | This Paper | GSE173682 | |
| scRNA-seq (raw data) | This Paper | phs002340.v1.p1 | |
| scATAC-seq (raw data) | This Paper | phs002340.v1.p1 | |
| Normal ovarian epithelial H3K27ac ChIP-seq peaks | Coetzee et. al., 2015 | GSE68104 | |
| Normal fallopian tube H3K27ac ChIP-seq peaks | Coetzee et. al., 2015 | GSE68104 | |
| Experimental models: Cell lines | |||
| Human: NIH:OVCAR-3 [OVCAR3] | ATCC | Cat#HTB-161, RRID: CVCL_0465 | |
| Human: HEK-293T | ATCC | Cat#CRL-3216, RRID: CVCL_0063 | |
| Experimental models: Organisms/strains | |||
| Human patients consented to participation in ‘Genomics of Ovarian and Endometrial Cancers’ study at the UNC Cancer Hospital (IRB Protocol 18–3198) | This Paper | Table 1, Table S1 | |
| Oligonucleotides | |||
| See Table S6, Table S7 and Table S8 | |||
| Recombinant DNA | |||
| Lenti-dCas9-KRAB-blast vector | Xie et al., 2017 | Addgene #89567 | |
| psPAX2 | Gift from Didier Trono | Addgene #12260 | |
| pMD2.G | Gift from Didier Trono | Addgene #12259 | |
| pSpCas9(BB)-2A-Puro (pX459) v2.0 | Ran et al., 2013 | Addgene #62988 | |
| pX-sgRNA-eGFP-MI | This paper | n/a | |
| Software and algorithms | |||
| Code used to analyze data presented in this paper | This Paper | 10.5281/zenodo.5546110 | |
| Prism (v9.0.0) | GraphPad | www.graphpad.com | |
| R (v4.0.2 or v4.0.3) | The R Project for Statistical Computing | https://www.r-project.org/ | |
| Seurat (v3.2.0 or v3.2.1) | Stuart et al., 2019 | https://satijalab.org/seurat/index.html | |
| ArchR (v0.9.5) | Granja et al., 2021 | https://www.archrproject.com/ | |
| mclust (v5.4.6 or v5.4.7) | Scrucca et al., 2016 | https://cran.r-project.org/web/packages/mclust/index.html | |
| scater (v1.17.5 or v1.18.6) | McCarthy et al., 2017 | https://bioconductor.org/packages/release/bioc/html/scater.html | |
| DESeq2 (v1.29.13 or v1.30.1) | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| inferCNV (v1.4.0 or v1.6.0) | Tickle, 2019 | http://www.bioconductor.org/packages/release/bioc/html/infercnv.html | |
| DoubletDecon (v1.1.5 or v1.1.6) | DePasquale et al., 2019 | https://github.com/EDePasquale/DoubletDecon | |
| DoubletFinder (v2.0.3) | McGinnis et al., 2019 | https://github.com/chris-mcginnis-ucsf/DoubletFinder | |
| GSVA (v1.36.1 or v1.36.2) | Hanzelmann et al., 2013 | http://bioconductor.org/packages/release/bioc/html/GSVA.html | |
| ggplot2 (v3.3.2 or v3.3.3) | Wickham, 2016 | https://cran.r-project.org/web/packages/ggplot2/index.html | |
| ComplexHeatmap (v2.4.3 or v2.6.2) | Gu et al., 2016 | https://jokergoo.github.io/ComplexHeatmap-reference/book/ | |
| Cell Ranger (v3.1.0) | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation | |
| Cell Ranger ATAC (v1.2.0) | 10x Genomics | https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation | |
| MEME suite (v4.12.0) | Bailey et al, 2009 | https://meme-suite.org/meme/index.html | |
| Python (v3.6.10) | Python Software Foundation | https://www.python.org/ | |
| Biopython (v1.78) | Python tools for computational biology | https://biopython.org / | |
| scikit-learn (v0.23.2) | Machine Learning in Python | https://scikit-learn.org/stable/ | |
| scipy (v1.5.2) | Fundamental Algorithms for Scientific Computing in Python | https://www.scipy.org/ | |