KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | ||
| Puromycin | Sigma | Cat#P8833 |
| Blasticidin | Invivogen | Cat#Ant-bl-1 |
| Critical Commercial Assays | ||
| LM-seq protocol | Hou et al., 2015 | |
| Maxima H Minus Reverse Transcriptase | Thermo Fisher | Cat#EP0753 |
| KAPA HiFi HS | KAPA | Cat#KK2502 |
| CellTiter-Glo Luminescent Cell Viability Assay | Promega | Cat#G7572 |
| GE Healthcare Sera-Mag Magnetic SpeedBeads | Thermo Fisher | Cat#09-981-121 |
| QIAGEN MinElute PCR purification Kit | QIAGEN | Cat#28004 |
| Gibson Assembly Master Mix | NEB | Cat#E2611L |
| 10X genomics Chromium Single Cell 3′ Kit V2 | 10X Genomics | Cat#PN-120237 |
| 10X Genomics Chromium Single Cell A Chip Kit | 10X Genomics | Cat#PN-120236 |
| 10X Genomics Chromium i7 Multiplex Kit | 10X Genomics | Cat#PN-1000009 |
| Bacterial and Viral Strains | ||
| Endura ElectroCompetent Cells | Lucigen | Cat#60242–2 |
| Stellar Competent Cells | Clonetech | Cat#636766 |
| Deposited Data | ||
| Single-cell RNA-seq Data | This paper | GEO: GSE129837 |
| RNA-seq Data | This paper | GEO: GSE129837 |
| Experimental Models: Cell Lines | ||
| K562 cells | ATCC | ATCC CCL243 |
| 293T cells | ATCC | ATCC CRL-3216 |
| Recombinant DNA | ||
| Plasmid: pMD2.G | Addgene | Addgene 12259 |
| Plasmid: psPAX2 | Addgene | Addgene 12260 |
| Plasmid: lenti-dCas9-KRAB-Blast | Addgene | Addgene 89567 |
| Plasmid: CROPseq-Guide-puro | Addgene | Addgene 86708 |
| Sequence-Based Reagents | ||
| sgRNA Oligos | Table S1 | N/A |
| Custom primers for library construction | Table S1 | N/A |
| qPCR primers | Table S1 | N/A |
| Software and Algorithms | ||
| Star | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Picard | Broad Institute | https://broadinstitute.github.io/picard/ |
| edgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| FeatureCounts | Liao et al., 2014 | http://bioinf.wehi.edu.au/featureCounts/ |
| 10X Genomics Cellranger V2.1.0 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| NetworkX | https://networkx.github.io | |
| Cytoscape | https://cytoscape.org | |
| GSEApy | https://github.com/zqfang/GSEApy/blob/master/docs/introduction.rst | |
| Mosaic-seq pipeline | This Paper | https://github.com/russellxie/Global-analysis-K562-enhancers |
| Other | ||
| Illumina NextSeq 500 instrument | Illumina | N/A |
| Agilent 2200 TapeStation instrument | Agilent | N/A |
| Qubit Fluorometric Quantitation instrument | Thermo Fisher | N/A |