KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| H3K27me3 Monoclonal Antibody (G.299.10) | Invitrogen | Cat#MA5-11198 |
| Anti-Histone H3 (acetyl K27) antibody | Abcam | Cat#ab4729 |
| Phospho-Rpb1 CTD (Ser2) (E1Z3G) Rabbit mAb | Cell Signaling Technology | Cat#13499 |
| Rabbit IgG | Abcam | Ab37415 |
| Bacterial and virus strains | ||
| BL21 DE3 pLysS bacteria | Novagen | Cat#69451 |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| Dynabeads His-Tag Isolation and Pulldown | Invitrogen | Cat#10103D |
| Concanavalin A coated magnetic beads | Polysciences | Cat#21-1401 |
| Histidine tagged pA-Tn5 | In this study | N/A (produced in Fazzio lab) |
| Critical commercial assays | ||
| AMPure XP beads | Beckman Coulter | Cat#A63881 |
| Qubit dsDNA HS Assay Kit | Invitrogen | Cat#Q32854 |
| NextSeq 500/550 High Output Kit v2.5 (150 Cycles) | Illumina | Cat#20024906 |
| Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 | 10X genomics | Cat#CG000209 |
| Deposited data | ||
| Raw and Analyzed data | GEO | GSE171554 |
| Code for sequencing data analysis | Zenodo | DOI: 10.5281/zenodo.5507375 |
| Experimental models: cell lines | ||
| E14 mouse embryonic stem cell line | Panning Lab, UCSF | RRID: CVCL_C320 |
| 5-4 mouse trophoblast stem cell line | Kalantry Lab, University of Michigan | N/A |
| Experimental models: organisms/strains | ||
| Oligonucleotides | ||
| See Table S1 for the sequences of DNA oligonucleotides used in multi-CUT&Tag experiments | In this study | N/A |
| Recombinant DNA | ||
| Software and algorithms | ||
| novoBarcode | Novocraft | http://www.novocraft.com/documentation/novobarcode/. |
| Bowtie 2, version 2.4.1 | Johns Hopkins University | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools, version 1.5 | SAMtools | http://samtools.sourceforge.net/ |
| Picard | Broad Institute | http://broadinstitute.github.io/picard/ |
| HOMER software suite, v4.11 | UCSD | http://homer.ucsd.edu/homer/ |
| cellranger-atac, version 1.1.0 | 10X genomics | https://support.10xgenomics.com/single-cell-atac/software/release-notes/1-1 |
| Cutadapt, version1.9 | Martin, 2011 | https://cutadapt.readthedocs.io/en/v1.9/guide.html |
| Bedtools, version 2.28.0 | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/content/installation.html |
| Macs2, version 1.4.2 | Zhang et al., 2008 | https://bioweb.pasteur.fr/packages/pack@macs@1.4.2 |
| Seurat, version 3.1.4 | Stuart et al., 2019 | https://github.com/satijalab/seurat/ |
| Other | ||
| Detailed protocol for the preparation of multi-CUT&Tag libraries | In this study | See Supplemental Information |