Skip to main content
. Author manuscript; available in PMC: 2022 Oct 21.
Published in final edited form as: Mol Cell. 2021 Oct 21;81(20):4319–4332.e10. doi: 10.1016/j.molcel.2021.09.026

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Human normal breast tissue samples Baylor College of Medicine N/A
Chemicals, peptides, and recombinant proteins
Anti-mouse PD-L1 Bio X Cell BE0101
Talazoparib Selleck S7048; CAS: 1207456-01-6
Carboplatin Auromedics 55150-386-01
Paclitaxel MDACC pharmacy PremierProRX
Tris-HCl (pH7.4) Sigma T2194
Tween-20 Andwin Scientific NC9022994
Nonidet P40 Substitute Sigma 74385
NaCl Invitrogen AM9760G
MgCl2 Invitrogen AM9530G
Digitonin Invitrogen BN2006
2-mercaptoethanol Gibco 21985023
RPMI-1640 ATCC 30–2001
IMDM ATCC 30–2005
DMEM Sigma D5796
FBS Sigma F0926
Penicillin-streptomycin Corning 30-002-Cl
Collagenase A Sigma 11088793001
TrypLE Express Enzyme (1X), phenol red Fisher 12605010
Trypsin-EDTA (0.25%) Corning 25053CI
Ultrapure BSA Ambion AM2616
10x MACS RBC lysis buffer MACS Miltenyi Biotec 130-094-183
DMEM F12/HEPES Gibco 113300
BSA fraction V Gibco 15260037
Creative Enzyme Tn5 Creative Enzyme NATE-1629
RNase Inhibitor NEB M0314L
Critical commercial assays
Chromium Single Cell ATAC Library & Gel Bead Kit 10X Genomics PN-1000110
Chromium Chip E Single Cell ATAC Kit 10X Genomics PN-1000155
Chromium i7 Multiplex Kit N, Set A 10X Genomics PN-1000084
Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit 10X Genomics PN-1000175
Chromium Next GEM Chip H Single Cell Kit 10X Genomics PN-1000161
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10X Genomics PN-1000283
Chromium Next GEM Chip J Single Cell Kit 10X Genomics PN-1000234
Dual Index Kit TT Set A 10X Genomics PN-1000215
Illumina Tagment DNA TDE1 Enzyme and Buffer Kit Illumina 20034198
Deposited data
Raw data files and processed data files This manuscript GEO: GSE162798
Experimental models: cell lines
Human: K562 ATCC ATCC: CCL-243
Mouse: A20 ATCC ATCC: TIB-208
Human: MDA-MB-231 MD Anderson Characterized Cell Line Core Facility N/A
Human: MDA-MB-436 MD Anderson Characterized Cell Line Core Facility N/A
Mouse: LKR13 MD Anderson Characterized Cell Line Core Facility N/A
Experimental models: organisms/strains
Mouse: 129S Jackson Laboratory 002448
Oligonucleotides
SBOs, see Table S1 This manuscript N/A
TruSeq RPIX primer: 5’-CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ IDT N/A
P5 Adaptor: 5’-AATGATACGGCGACCACCGAGATCTACAC-3’ IDT N/A
Read 1 Primer: 5’-TCGTCGGCAGCGTCTGGTATCAACGCAGAGTAG-3’ IDT N/A
I5 Index Primer: 5’-CTACTCTGCGTTGATACCAGACGCTGCCGACGA-3’ IDT N/A
SNuBar_RNA-I7–1bc: 5’-CGAGCCCACGAGACCCTTGGCACCCGAGAATTCCAAGTATGCTCCTTCCGTCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3’ IDT N/A
SNuBar_RNA-I7–2bc: 5’-CGAGCCCACGAGACCCTTGGCACCCGAGAATTCCAGCGACGCAGATAAACCCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3’ IDT N/A
SNuBar_RNA-I7–3bc: 5’-CGAGCCCACGAGACCCTTGGCACCCGAGAATTCCACCATCTGAGGTGTCAGCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3’ IDT N/A
SNuBar_RNA-I7–4bc: 5’-CGAGCCCACGAGACCCTTGGCACCCGAGAATTCCACGTTGTACTCAGATCTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3’ IDT N/A
bcP: 5’-CCTTGGCACCCGAGAATTCCA-3’ IDT N/A
InPE 1: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ IDT N/A
Tn5-ME-Ap: /5phos/TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’ IDT NA
Tn5-ME-rev: /5phos/CTGTCTCTTATACACATCT IDT NA
Tn5-ME-B: 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3’ IDT NA
Software and algorithms
CellRanger ATAC (v1.2.0) 10X Genomics https://github.com/10XGenomics/cellranger-atac
CellRanger ARC (v1.0.0) 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
CellRanger (v4.0.0) 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
CITE-seq-Count (v1.4.3) DOI: 10.5281/zenodo.2590196 https://github.com/Hoohm/CITE-seq-Count
ArchR (v0.9.5) Granja et al., 2021 https://github.com/GreenleafLab/ArchR/tree/cadc5844259aee51a8e42afcf8ab72c5fc32632d
Signac (v1.1.1) Stuart et al., 2020 https://github.com/timoast/signac/
Demuxlet (implemented in ‘popscle’) Kang et al., 2017 https://github.com/statgen/popscle/tree/4b6a88a7b38da04dd7c3544df29240748f54c602
souporcell Heaton et al., 2020 https://github.com/wheaton5/souporcell
chromVAR (v1.12.0) Schep, A., Wu, B., Buenrostro, J. et al., 2017 https://github.com/GreenleafLab/chromVAR
Harmony (v1.0) Korsunsky, I., Millard, N., Fan, J. et al., 2019 https://github.com/immunogenomics/harmony
clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
EnsDb.Hsapiens.v75 NA https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v75.html
EnsDb.Mmusculus.v79 NA http://www.bioconductor.org/packages//release/data/annotation/html/EnsDb.Mmusculus.v79.html
chromVARmotifs NA https://github.com/GreenleafLab/chromVARmotifs
MACS2 Zhang, Y., Liu, T., Meyer, C.A. et al., 2008 https://pypi.org/project/MACS2/
Seurat (v4.0.0) Hao*, Hao*, et al., Cell 2021 https://github.com/satijalab/seurat/
Ggrastr (v0.2.1) NA https://github.com/VPetukhov/ggrastr
ComplexHeatmap (v2.6.2) Zuguang Gu, et al., 2016 https://github.com/jokergoo/ComplexHeatmap
Other
Detailed protocols (SNuBar-ATAC and SNuBar-ARC) This paper Methods S1