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 |
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Bacterial and virus strains |
BL21 DE3 pLysS bacteria |
Novagen |
Cat#69451 |
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Biological samples |
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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) |
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Critical commercial assays |
AMPure XP beads |
Beckman Coulter |
Cat#A63881 |
Qubit dsDNA HS Assay Kit |
Invitrogen |
Cat#Q32854
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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
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Deposited data |
Raw and Analyzed data |
GEO |
GSE171554 |
Code for sequencing data analysis |
Zenodo |
DOI: 10.5281/zenodo.5507375
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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 |
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Experimental models: organisms/strains |
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Oligonucleotides |
See Table S1 for the sequences of DNA oligonucleotides used in multi-CUT&Tag experiments |
In this study |
N/A |
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Recombinant DNA |
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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
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Samtools, version 1.5 |
SAMtools |
http://samtools.sourceforge.net/
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Picard |
Broad Institute |
http://broadinstitute.github.io/picard/
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HOMER software suite, v4.11 |
UCSD |
http://homer.ucsd.edu/homer/
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cellranger-atac, version 1.1.0 |
10X genomics |
https://support.10xgenomics.com/single-cell-atac/software/release-notes/1-1
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Cutadapt, version1.9 |
Martin, 2011
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https://cutadapt.readthedocs.io/en/v1.9/guide.html
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Bedtools, version 2.28.0 |
Quinlan and Hall, 2010
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https://bedtools.readthedocs.io/en/latest/content/installation.html
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Macs2, version 1.4.2 |
Zhang et al., 2008
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https://bioweb.pasteur.fr/packages/pack@macs@1.4.2
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Seurat, version 3.1.4 |
Stuart et al., 2019
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https://github.com/satijalab/seurat/
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Other |
Detailed protocol for the preparation of multi-CUT&Tag libraries |
In this study |
See Supplemental Information
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