KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet 421 anti-human CD24 Antibody (clone ML5) | BioLegend | Cat# 311121; RRID: AB_10915556 |
| Brilliant Violet 421 Mouse IgG2a, κ Isotype Ctrl Antibody (clone MOPC-173) | BioLegend | Cat# 400259; RRID: AB_10895919 |
| APC anti-human CD24 Antibody (clone ML5) | BioLegend | Cat# 311117; RRID: AB_1877150 |
| APC Rat IgG2a, κ Isotype Ctrl (clone RTK2758) | BioLegend | Cat# 400511; RRID: AB_2814702 |
| Bacterial and Virus Strains | ||
| AAV9-PB-SRT-tdTomato | Joseph D. Dougherty (Cammack et al., 2020) | N/A |
| AAV9-HyPBase | Joseph D. Dougherty (Cammack et al., 2020) | N/A |
| Lenti-dCas9-KRAB | This study | N/A |
| Lenti-BRD4-CRISPRi | This study | N/A |
| Lenti-NT-CRISPRi | This study | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DMEM | GIBCO | Cat# 11965-084 |
| Antibiotic-Antimycotic (100X) | GIBCO | Cat# 15240-062 |
| FBS | Peak Serum | Cat# PS-FB3 |
| RPMI 1640 Medium | GIBCO | Cat# 11875-085 |
| Lipofectamine 3000 Transfection Reagent | Invitrogen | Cat# L3000015 |
| Trypsin-EDTA solution | Sigma-Aldrich | Cat# T4049 |
| DPBS, no calcium, no magnesium | GIBCO | Cat# 14190-136 |
| RNAprotect Cell Reagent | QIAGEN | Cat# 76526 |
| 2-Mercaptoethanol | GIBCO | Cat# 21985-023 |
| RNase-Free DNase Set | QIAGEN | Cat# 79254 |
| Maxima H Minus Reverse Transcriptase | Thermo Scientific | Cat# EP0752 |
| Advantage® UltraPure PCR Deoxynucleotide Mix | Takara Bio | Cat# 639125 |
| RNaseOUT Recombinant Ribonuclease Inhibitor | Invitrogen | Cat# 10777019 |
| TransIT®-LT1 Transfection Reagent | Mirus | Cat# MIR2304 |
| RNase H | New England BioLabs | Cat# M0297S |
| HiFi HotStart ReadyMix (2X) | Kapa Biosystems | Cat# KK2601 |
| AMPure XP beads | Beckman Coulter | Cat# A63880 |
| Puromycin dihydrochloride | Sigma-Aldrich | Cat# P8833 |
| Crystal violet | Sigma-Aldrich | Cat# C0775 |
| Methanol | Fisher Scientific | Cat# A452-4 |
| Formaldehyde | Fisher Scientific | Cat# BP531-500 |
| High Sensitivity D1000 Reagents | Agilent | Cat# 5067-5585 |
| Ficoll PM400 (Dry Powder) | GE Healthcare | Cat# 17030010 |
| NxGen® RNase Inhibitor | Lucigen | Cat# 30281-1 |
| Dynabeads MyOne Silane | Life Technologies | Cat# 37002D |
| IDTE pH 8.0 (1X TE Solution) | IDT | Cat# 11-05-01-13 |
| High Sensitivity D5000 Reagents | Agilent | Cat# 5067-5593 |
| NEBuffer 2 | New England BioLabs | Cat# B7002S |
| Buffer EB | QIAGEN | Cat# 19086 |
| Hibernate-A Medium | GIBCO | Cat# A1247501 |
| D-(+)-Trehalose dihydrate | Sigma-Aldrich | Cat# T9531 |
| B-27 Supplement (50X), serum free | GIBCO | Cat# 17504044 |
| 0.5M EDTA, pH 8.0 | Coming | Cat# 46-034-CI |
| Papain, Lyophilized | Worthington Biochemical | Cat# LS003118 |
| Deoxyribonuclease I, Filtered | Worthington Biochemical | Cat# LS002060 |
| Trypsin Inhbitor, Ovomucoid | Worthington Biochemical | Cat# LS003087 |
| Bovine Serum Albumin | Sigma-Aldrich | Cat# A9418 |
| OptiPrep Density Gradient Medium | Sigma-Aldrich | Cat# D1556 |
| HBSS (10X) | GIBCO | Cat# 14185052 |
| Magnesium chloride | Sigma-Aldrich | Cat# M4880 |
| Magnesium sulfate | Sigma-Aldrich | Cat# M2643 |
| Calcium chloride dihydrate | Sigma-Aldrich | Cat# C7902 |
| D-(+)-Glucose | Sigma-Aldrich | Cat# G7021 |
| Dimethyl sulfoxide (DMSO) | Sigma-Aldrich | Cat# D2650 |
| Cell Staining Buffer | BioLegend | Cat# 420201 |
| Annexin V Binding Buffer | BioLegend | Cat# 422201 |
| SuperScript VILO cDNA Synthesis Kit | Invitrogen | Cat# 11754250 |
| PowerUp SYBR Green Master Mix | Applied Biosystems | Cat# 25742 |
| (+)-JQ1 | Selleck Chemicals | Cat# S7110 |
| Propidium iodide (PI) | Invitrogen | Cat# P3566 |
| Hoechst 33342 | Thermo Scientific | Cat# 62249 |
| Blasticidin S HCl | GIBCO | Cat# A1113903 |
| Lenti-X Concentrator | Takara Bio | Cat# 631232 |
| Lipofectamine 2000 Transfection Reagent | Invitrogen | Cat# 11668030 |
| Polybrene Infection / Transfection Reagent | Sigma-Aldrich | Cat# TR-1003 |
| Esp3I | New England BioLabs | Cat# R0734S |
| T4 DNA Ligase | New England BioLabs | Cat# M0202S |
| IMDM | GIBCO | Cat# 12440046 |
| Penicillin-Streptomycin (10,000 U/mL) | GIBCO | Cat# 15140122 |
| Imatinib mesylate | Sigma-Aldrich | Cat# SML1027 |
| Lovastatin | Sigma-Aldrich | Cat# M2147 |
| Nocodazole | Sigma-Aldrich | Cat# M1404 |
| CVT-313 | Sigma-Aldrich | Cat# 238803 |
| RO-3306 | Sigma-Aldrich | Cat# SML0569 |
| Annexin V-FITC | BioLegend | Cat# 640905 |
| Critical Commercial Assays | ||
| Neon Transfection System 100 μL Kit | Invitrogen | Cat# MPK10025 |
| RNeasy Plus Mini Kit | QIAGEN | Cat# 74134 |
| Qubit RNA HS Assay Kit | Invitrogen | Cat# Q32852 |
| Qubit dsDNA HS Assay Kit | Invitrogen | Cat# Q32851 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat# FC-131-1024 |
| High Sensitivity D1000 ScreenTape | Agilent | Cat# 5067-5584 |
| Chromium Single Cell 3’ Library & Gel Bead Kit v2 | 10x Genomics | Cat# PN-120267 |
| High Sensitivity D5000 ScreenTape | Agilent | Cat# 5067-5592 |
| Nextera Mate Pair Library Prep Kit | Illumina | Cat# FC-132-1001 |
| Deposited Data | ||
| K562 CpG islands | Richard Myers | GEO: GSM1014203 |
| HCT-116 SP1 ChIP-seq | Richard Myers | ENCODE: ENCFF000PCT |
| HCT-116 CTCF ChIP-seq | Richard Myers | ENCODE: ENCFF000ZC |
| HCT-116 ChIP-seq input control (SP1, CTCF) | Richard Myers | ENCODE: ENCFF000PBO |
| HCT-116 BRD4 ChIP-seq | Ron Firestein | SRA: SRR2481799 |
| HCT-116 ChIP-seq input control (BRD4) | Ron Firestein | SRA: SRR2481800 |
| HCT-116 H3K27ac ChIP-seq | Bradley Bernstein | ENCODE: ENCFF082JPN, ENCFF176BXC |
| HCT-116 H3K4me1 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF088BWP, ENCFF804MJI |
| HCT-116 H3K4me2 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF936MMN, ENCFF93700L |
| HCT-116 H3K4me3 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF1830ZI, ENCFF659FPR |
| HCT-116 H3K9me2 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF7600ZN, ENCFF565FDP |
| HCT-116 H3K9me3 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF578MDZ, ENCFF033X0G |
| HCT-116 H3K27me3 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF281SBT, ENCFF124GII |
| HCT-116 H3K36me3 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF850EAH, ENCFF312RKB |
| HCT-116 H3K79me2 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF865KPW, ENCFF947YPU |
| HCT-116 H4K20me1 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF070JDY, ENCFF334HHB |
| HCT-116 ChIP-seq input control (H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K9me2, H3K9me3, H3K27me3, H3K36me3, H3K79me2, H4K20me1) | Bradley Bernstein | ENCODE: ENCFF048Z0Q, ENCFF827YXC |
| HCT-116 H3K9ac ChIP-seq | Bradley Bernstein | ENCODE: ENCFF408RRT |
| HCT-116 ChIP-seq input control (H3K9ac) | Bradley Bernstein | ENCODE: ENCFF413RQG |
| K562 BRD4 ChIP-seq | Bradley Bernstein | ENCODE: ENCFF335PHG |
| K562 H3K27ac ChIP-seq | Bradley Bernstein | ENCODE: ENCFF000BXH |
| K562 ChIP-seq input control (BRD4, H3K27ac) | Bradley Bernstein | ENCODE: ENCFF000BWK |
| K562 SP1 ChIP-seq | Michael Snyder | ENCODE: ENCFF002DPL, ENCFF002EGC |
| K562 ChIP-seq input control (SP1) | Michael Snyder | ENCODE: ENCFF002EGI, ENCFF002EGA |
| HepG2 FOXA2 ChIP-seq | Richard Myers | ENCODE: ENCFF000PIX |
| HepG2 ChIP-seq input control (FOXA2) | Richard Myers | ENCODE: ENCFF000P0V |
| OCM-1A HyPBase DNA calling cards | Michael Onken | https://doi.org/10.1186/s12920-018-0424-0 |
| OCM-1A BAP1-HyPBase DNA calling cards | Michael Onken | https://doi.org/10.1186/s12920-018-0424-0 |
| OCM-1A RNA-seq (BAP1 and control shRNA) | Michael Onken | GEO: GSE110193 |
| Mouse cortex H3K27ac ChIP-seq | Michael Greenberg | SRA: SRR6129714 |
| Mouse cortex ChIP-seq input control (H3K27ac) | Michael Greenberg | SRA: SRR6129695 |
| K562 RNA Pol II ChIA-PET | Yijun Ruan | ENCODE: ENCFF000KYH |
| HCT-116 DNase-seq | John Stamatoyannopoulos | ENCODE: ENCFF001DCK |
| HCT-116 ATAC-seq | Sriharsa Pradhan | SRA: SRR5453778 |
| HCT-116 ATAC-seq control | Michael Guertin | GEO: GSE92674 |
| HCT-116 CpG islands | Richard Myers | GEO: GSM1014209 |
| Sequencing data and processed output | This study | GEO: GSE148448 |
| Experimental Models: Cell Lines | ||
| Neuro-2a (N2a) | ATCC | Cat# CCL-131 |
| K-562 | ATCC | Cat# CCL-243 |
| Hep G2 | ATCC | Cat# HB-8065 |
| OCM-1A | Michael Onken (Yen et al., 2018) | N/A |
| HCT 116 | ATCC | Cat# CCL-247 |
| 293T/17 [HEK293T/17] | ATCC | Cat# CRL-11268 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | Joseph D. Dougherty (Cammack et al., 2020) | N/A |
| Oligonucleotides | ||
| Primers and oligonucleotides | This study, see Table S4 | N/A |
| Recombinant DNA | ||
| pRM1024: PBase | This study | N/A |
| pRM1114: HyPBase | This study | N/A |
| pRM1023: SP1-PBase | This study | N/A |
| pRM1677: SP1 -HyPBase | This study | N/A |
| pRM1882: FOXA2-HyPBase | This study | N/A |
| pRM1863: BAP1-HyPBase | This study | N/A |
| pRM1304: PB-SRT-Puro | This study | RRID: Addgene_154884 |
| pRM1535: PB-SRT-tdTomato | This study | RRID: Addgene_154885 |
| pCMV(CAT)T7-SB100 | Zsuzsanna Izsvak | RRID: Addgene_34879 |
| pRM1665: SP1-SB100X | This study | RRID: Addgene_154887 |
| pRM1668: SB-SRT-Puro | This study | RRID: Addgene_154888 |
| pRM1217: AAV-HyPBase | Joseph D. Dougherty (Cammack et al., 2020) | N/A |
| pRM1648: AAV-PB-SRT-tdTomato | Joseph D. Dougherty (Cammack et al., 2020) | RRID: Addgene_154889 |
| pUC19 Vector | New England BioLabs | Cat# N3041S |
| Lenti-dCas9-KRAB-blast | Gary Hon | RRID: Addgene_89567 |
| sgOpti | Eric Lander & David Sabatini | RRID: Addgene_85681 |
| pMD2.G | Didier Trono | RRID: Addgene_12259 |
| psPAX2 | Didier Trono | RRID: Addgene_12260 |
| pRM1889: BRD4 CRISPRi plasmid | This study | RRID: Addgene_154890 |
| pRM1890: Non-targeting CRISPRi plasmid | Robi D. Mitra (Lalli et al., 2019) | RRID: Addgene_154891 |
| Software and Algorithms | ||
| cutadapt 1.16 | Martin, 2011 | RRID: SCR_011841 |
| NovoAlign 3 | Novocraft Technologies | RRID: SCR_014818 |
| Cell Ranger 2.1.0 | 10x Genomics | RRID: SCR_017344 |
| scanpy 1.3.7 | Wolf etal., 2018 | RRID: SCR_018139 |
| Drop-seq tools 1.11 | Macosko et al., 2015 | RRID: SCR_018142 |
| astropy 3.2.1 | Robitaille et al., 2013 | RRID: SCR_018148 |
| WashU Human Epigenome Browser 46 | Zhou et al., 2011 | RRID: SCR_006208 |
| MEME-ChIP 4.11.2 | Machanick and Bailey, 2011 | RRID: SCR_001783 |
| Tomtom 5.1.0 | Gupta et al., 2007 | RRID: SCR_001783 |
| MACS 1.4.1 | Zhang et al., 2008 | RRID: SCR_013291 |
| BEDTools 2.27.1 | Quinlan and Hall, 2010 | RRID: SCR_006646 |
| NumPy 1.17.2 | Oliphant, 2015 | RRID: SCR_008633 |
| SciPy 1.4.1 | Virtanen et al., 2020 | RRID: SCR_008058 |
| statsmodels 0.10.1 | Seabold and Perktold, 2010 | RRID: SCR_016074 |
| matplotlib 3.0.3 | Hunter, 2007 | RRID: SCR_008624 |
| deeptools 3.0.1 | Ramírez et al., 2016 | RRID: SCR_016366 |
| ChromHMM 1.15 | Ernst et al., 2011 | RRID: SCR_018141 |
| liftOver | Hinrichs et al., 2006 | RRID: SCR_018160 |
| FlowCal 1.2.0 | Castillo-Hair et al., 2016 | RRID: SCR_018140 |
| PANTHER 14.0 | Mi etal., 2017 | RRID: SCR_004869 |
| ROSE 0.1 | Whyte et al., 2013 & Lovén et al., 2013 | RRID: SCR_017390 |
| FlowJo Software for Mac Version 10 | Becton, Dickson and Company | RRID: SCR_008520 |
| Multcomp 1.4-12 | Hothorn et al., 2008 | RRID: SCR_018255 |
| Custom calling card code | This study | https://github.com/arnavm/calling_cards |
| Other | ||
| Qubit® 3.0 Fluorometer | Thermo Fisher | Cat# Q33216 |
| 4200 TapeStation System | Agilent | Cat# G2991AA |
| E220 Focused-ultrasonicator | Covaris | N/A |
| MasterCycler Pro PCR System | Eppendorf | Cat# 950030010 |
| Attune NxT Flow Cytometer | Thermo Fisher | N/A |
| CytoFLEX S | Beckman-Coulter | Cat# B75442 |
| QuantStudio | Applied Biosystems | Cat# A28567 |
| Protocol: Mammalian Calling Cards Quick Start Guide | This study | https://doi.org/10.17504/protocols.io.xurfnv6 |
| Protocol: Bulk Calling Cards Library Preparation | This study | https://doi.org/10.17504/protocols.io.xwhfpb6 |
| Protocol: Single Cell Calling Cards Library Preparation | This study | https://doi.org/10.17504/protocols.io.xwifpce |
| Protocol: Processing Bulk Calling Card Sequencing Data | This study | https://doi.org/10.17504/protocols.io.xwjfpcn |
| Protocol: Processing Single Cell Calling Card Sequencing Data | This study | https://doi.org/10.17504/protocols.io.4phgvj6 |
| Protocol: Calling Peaks on piggyBac Calling Card Data | This study | https://doi.org/10.17504/protocols.io.bb9xir7n |
| Protocol: Visualizing Calling Card Data on the WashU Epigenome Browser | This study | https://doi.org/10.17504/protocols.io.bca8ishw |