Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Fluorescence-activated cell sorting | ||
| anti-human CD15, APC | Biolegend | Cat# 301908 |
| anti-human CD3, PE-Dazzle594 | Biolegend | Cat# 300450 |
| anti-human CD45, Pacific blue | Biolegend | Cat# 304022 |
| anti-human CD66b, PE-CY7 | Biolegend | Cat# 305116 |
| anti-human TruStain FcX | Biolegend | Cat# 422302 |
| Multiplexed Immunofluorescence | ||
| anti-human CD138 (MI15) | Leica | Cat# PA0088 |
| anti-human CD163 (10D6) | Leica | Cat# CD163-L-CE |
| anti-human CD68 (KP1) | Biogenex | Cat# AM416-5M |
| anti-human CD8 (4B11) | Leica | Cat# CD8-4B11-L-CE |
| anti-human HMB45 9HMB-45) | Cell Marque | Cat# 282M-95 |
| anti-human NCAM1 (123C3) | Invitrogen | Cat# MA1-06801 |
| anti-human SOX10 (BC34) | BioCare | Cat# ACI3099C |
| Bacterial and virus strains | ||
| C3013 Competent Cells | New England Biolabs | Cat# C3013I |
| Biological samples | ||
| Fresh human melanoma brain metastases | This study | Table S1 |
| Frozen human melanoma brain and extracranial metastases | This study | Table S1 |
| Formalin-fixed paraffin-embedded melanoma brain and liver metastases | This study | Table S1 |
| Chemicals, peptides, and recombinant proteins | ||
| 10% NP-40 Surfact-Amps Detergent Solution | Thermo Fisher Scientific | Cat# 28324 |
| 2-mercaptoethanol | Thermo Fisher Scientific | Cat# 21-985-023 |
| 4’,6-diamidino-2-phenylindole (DAPI) | Akoya Bioscience | Cat# NEL821001KT |
| 70 μm cell strainer | Corning | Cat# 431751 |
| Acetic Acid | Thermo Fisher Scientific | Cat# A38S-500 |
| ACK buffer | Thermo Fisher Scientific | Cat# A1049201 |
| Amicon Ultra-4 Centrifugal Filters, 30kDa | EMD Millipore | Cat# UFC803024 |
| AMPure XP Beads | Beckman Coulter | Cat# A63880 |
| Bambanker | Bulldog Bio | Cat# BB01 |
| Benzonase Nuclease | Millipore Sigma | Cat# E1014-25KU |
| BOND Dewax Solution | Leica | Cat# AR9222 |
| BOND Epitope Retrieval Solution 1, pH 6 | Leica | Cat# AR9961 |
| BOND Epitope Retrieval Solution 2, pH 9 | Leica | Cat# AR9640 |
| Bovine serum albumin (BSA) | New England Biolabs | Cat# B9000S |
| CaCl2 1M | VWR | Cat# 97062-820 |
| Calcein AM | Invitrogen | Cat# C1430 |
| Chitin Resin | New England Biolabs | Cat# S6651L |
| Collagenase I | Worthington | Cat# LS004196 |
| cOmplete Protease Inhibitors | Millipore Sigma | Cat# 1167498001 |
| D1000 Reagents | Agilent Technologies | Cat# 5067-5583 |
| D1000 ScreenTape | Agilent Technologies | Cat# 5067-5582 |
| D5000 Reagents | Agilent Technologies | Cat# 5067-5589 |
| D5000 ScreenTape | Agilent Technologies | Cat# 5067-5588 |
| Dimethylformamide | Thermo Fisher Scientific | Cat# D119-500 |
| DMEM | Gibco | Cat# 11965092 |
| DNAse I | Worthington | Cat# LS002139 |
| DTT 1M | Millipore Sigma | Cat# 646563-10X.5ML |
| Econo Pac | BioRad | Cat# 7321010 |
| Econo-Column Chromatography Columns | BioRad | Cat# 7372512 |
| EDTA 0.5M | Thermo Fisher Scientific | Cat# AM9262 |
| Ethanol 99.5% 200 proof | Thermo Fisher Scientific | Cat# 615090010 |
| Falcon® Round-Bottom Tubes with Cell Strainer Cap | Thermo Fisher Scientific | Cat# 08-771-23 |
| Fetal Bovine Serum | Gibco | Cat# 10-437-028 |
| GlutaMax | Thermo Fisher Scientific | Cat# 35050061 |
| Glycerol | Thermo Fisher Scientific | Cat# BP229-1 |
| H2O (RNA/DNA clean) | Thermo Fisher Scientific | Cat# 10-977-015 |
| Hank's Balanced Salt Solution | Thermo Scientific | Cat# J67763.K2 |
| HEPES | Thermo Fisher Scientific | Cat# 15-630-106 |
| HEPES | Thermo Fisher Scientific | Cat# BP310-100 |
| Hoechst 33342 | Invitrogen | Cat# H3570 |
| Human Tumor Dissociation Kit | Miltenyi | Cat# 30-095-929 |
| Insulin-Transferrin-Selenium | Thermo Fisher Scientific | Cat# 41400-045 |
| IPTG | Thermo Fisher Scientific | Cat# BP1755-1 |
| Luria Broth | Thermo Fisher Scientific | Cat# BP9723-2 |
| MEM Non-essential Amino Acids | Gibco | Cat# 11140050 |
| MgCl2 1M | Thermo Fisher Scientific | Cat# AM9530G |
| MinElute Reaction Cleanup Kit | Qiagen | Cat# 28206 |
| NaCl 5M | Thermo Fisher Scientific | Cat# AM9759 |
| NEBNext High-Fidelity 2X PCR Master Mix | New England Biolabs | Cat# M0541S |
| NEBNext Ultra II RNA Library Prep Kit | New England Biolabs | Cat# E7420L |
| Odyssey Blocking Buffer | Li-Cor | Cat# 927-40000 |
| Opal 7-Color Automated IHC Staining Kit | Akoya Bioscience | Cat# NEL821001KT |
| Optimal cutting temperature compound (OCT) | Tissue-Tek, Sankura | Cat# 94-4583 |
| Optiprep Density Gradient Medium | Sigma Aldrich | Cat# D1556 |
| PBS | Thermo Fisher Scientific | Cat# 20-012-050 |
| PBS (10X) | Thermo Fisher Scientific | Cat# BP399-500 |
| Penicillin Streptomycin (10,000 U/mL) | Thermo Fisher Scientific | Cat# 15-140-122 |
| Plasmotest | InvivoGen | Cat# rep-pt1 |
| Qubit 1X dsDNA HS Assay Kit | Thermo Fisher Scientific | Cat# Q33230 |
| RNAeasy Plus | Qiagen | Cat# 74134 |
| RNAse OUT | Thermo Fisher Scientific | Cat# 10-777-019 |
| RPMI 1640 | Thermo Fisher Scientific | Cat# 21875034 |
| Slide-A-Lyzer Dialysis Cassete Kit, 10K MWCO | Thermo Fisher Scientific | Cat# 66807 |
| SPRIselect beads | Beckman Coulter | Cat# B23318 |
| SYBR Green I Nucleic Acid Gel Stain 10000x | Thermo Fisher Scientific | Cat# S7563 |
| Tris HCL pH7.5 1M | Thermo Fisher Scientific | Cat# 5567027 |
| Tris pH8.0 1M | Thermo Fisher Scientific | Cat# 15568-025 |
| Tris(hydroxymethyl)aminomethane | Millipore Sigma | Cat# 252859-100G |
| Triton X100 | Millipore Sigma | Cat# X100-500ML |
| Tween-20 | Sigma Aldrich | Cat# p-7949 |
| UltraPure Distilled Water | Thermo Fisher Scientific | Cat# 10977-023 |
| Vectashield HardSet Antifade mounting medium | Vector Laboratories | Cat# H-1400 |
| Zombie NIR viability dye | Biolegend | Cat# 423106 |
| Critical commercial assays | ||
| Chromium Single Cell 3’ reagents v3.0 | 10x genomics | Cat# 1000006 |
| Chromium Single Cell 5’ Library construction kit | 10x genomics | Cat# 1000020 |
| Chromium Single Cell V(D)J Enrichment Kit for human T cells | 10x genomics | Cat# 1000005 |
| Chromium Single Cell V(D)J Reagents | 10x genomics | Cat# 1000006 |
| Falcon™ FluoroBlok™ HTS 96-Well Insert Systems, 8.0 um pore | Thermo Fisher Scientific | Cat# 08-771-007 |
| Deposited data | ||
| sc/snRNA-seq data of brain and extracranial melanoma metastases | This study | GSE185386 |
| TCR-seq of melanoma brain metastases | This study | GSE185386 |
| SlideSeqV2 of brain and extracranial melanoma metastases | This study | GSE185386 |
| RNA-seq (patient-derived cell lines of brain and extracranial melanoma metastases) | This study | GSE185386 |
| ATAC-seq (patient-derived cell lines of brain and extracranial melanoma metastases) | This study | GSE185386 |
| Raw data generated using sc/snRNA-seq, TCR-seq, SlideSeqV2, RNA-seq, and ATAC-seq | This study | dbGaP (https://www.ncbi.nlm.nih.gov/gap) |
| RNA-seq (patient samples of brain and extracranial melanoma metastases) | Fischer at al., 2019 | DOI: 10.1158/2159-8290.CD-18-1489 |
| Whole-exome sequencing (patient samples of brain and extracranial melanoma metastases) | Fischer at al., 2019 | DOI: 10.1158/2159-8290.CD-18-1489 |
| Proteomics data (brain and extracranial melanoma metastases) | Kleffman et al., 2022 | https://massive.ucsd.edu/ (ID: MassIVE MSV000088814) |
| RNA-seq data (xenografts) | This study | Available upon request |
| Experimental models: Cell lines | ||
| 131/4-5B1 "5B1" | Cruz-Munoz et al, 2008 | Authenticated by STR analysis by ATCC |
| 113/6-4L "4L" | Cruz-Munoz et al, 2008 | Authenticated by STR analysis by ATCC |
| 12-273-BM "273-BM" | Eva Hernando, NYU | N/A |
| 12-273-LN "273-LN" | Eva Hernando, NYU | N/A |
| 2686 | MD Anderson | N/A |
| MaMel-134 | UK-Essen | N/A |
| MBM03 | This study | N/A |
| MBM05 | This study | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) | The Jackson Laboratory | Strain# 005557 |
| Oligonucleotides | ||
| Ad1_noMX | Buenrostro et al., 2013 | AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG |
| Ad2.1_NNNNNNNN | Buenrostro et al., 2013 | CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGT |
| Recombinant DNA | ||
| CMV-Luciferase-EF1α-copGFP | BD Biosciences | Cat# BLIV511PA-1 |
| pTXB1-Tn5 | Addgene | Cat# 60240 |
| Software and algorithms | ||
| Andromeda | Cox et al., 2011 | https://bioinformaticshome.com/tools/proteomics/descriptions/Andromeda.html |
| ARACNe-AP algorithm | Basso et al., 2005; Lachmann et al., 2016 | http://califano.c2b2.columbia.edu/aracne |
| biomaRt v2.46.3 | Durinck et al., 2009 | https://bioconductor.org/packages/biomaRt/ |
| Cell Ranger v6.1.1 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| CellBender v0.2.0 | Fleming et al., 2019 | https://github.com/broadinstitute/CellBender |
| CoBRA v2.0 | Qiu et al., 2021 | https://doi.org/10.1016/j.gpb.2020.11.007 |
| Conos v1.4.4 | Barkas et al., 2019 | https://github.com/kharchenkolab/conos |
| cutadapt v3.6 | Martin, 2011 | http://journal.embnet.org/index.php/embnetjournal/article/view/200 |
| deepTools2 v3.5.1 | Ramírez et al., 2016 | https://academic.oup.com/nar/article/44/W1/W160/2499308 |
| DESeq2 v1.34.0 | Love et al., 2014 | https://bioconductor.org/packages/DESeq2/ |
| Destiny v3.9.0 | Angerer et al., 2016 | https://github.com/theislab/destiny |
| DoubletFinder v2.0.3 | McGinnis et al., 2019 | https://github.com/chris-mcginnis-ucsf/DoubletFinder |
| FastQC v0.11.9 | Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Fastqscreen v.0.13.0 | Wingett and Andrews, 2018 | https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ |
| featureCounts v1.6.3 | Liao et al., 2014 | https://doi.org/10.1093/bioinformatics/btt656 |
| GmAMisc v1.2.0 | Alberti, 2021 | https://CRAN.R-project.org/package=GmAMisc |
| Harmony v0.1.0 | Korsunsky et al., 2019 | https://github.com/immunogenomics/harmony |
| hisat2 v2.2.1 | Kim et al., 2019 | https://www.nature.com/articles/s41587-019-0201-4 |
| hypeR v1.10.0 | Federico and Monti, 2020 | https://github.com/montilab/hypeR |
| ImageJ | ImageJ | https://imagej.nih.gov/ij/ |
| inferCNV v1.10.1 | Tirosh et al., 2016 | https://github.com/broadinstitute/inferCNV |
| inForm v2.5.1 | Akoya Biosciences | https://www.akoyabio.com/support/software/ |
| Kallisto v0.46.1 | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| LivingImage software | Xenogen Corp., Alameda, CA | http://www.perkinelmer.com/product/spectrum-200-living-image-v4series-1-128113 |
| MACS2 v2.2.7.1 | Feng et al., 2012 | https://www.nature.com/articles/nprot.2012.101 |
| MaxQuant v1.5.2.8 | Cox et al., 2008 | https://maxquant.org |
| MCMICRO | Schapiro et al., 2021 | https://mcmicro.org |
| Mesmer 0.3.0 | Greenwald et al., 2021 | https://hub.docker.com/r/vanvalenlab/deepcell-applications |
| MSigDB v7.4.1 | Dolgalev, 2021 | https://CRAN.R-project.org/package=msigdbr |
| Perseus | Tyanova et al., 2016 | http://www.perseus-framework.org |
| Phenochart v1.1.0 | Akoya Biosciences | https://www.akoyabio.com/support/software/ |
| Picard v2.18.20 | Broad Institute | https://broadinstitute.github.io/picard/ |
| ProjecTILs v1.0 | Andreatta et al., 2021 | https://github.com/carmonalab/ProjecTILs |
| Python v3.9.9 | Python Software Foundation | https://www.python.org |
| R v4.1.1 | The R Foundation | https://www.r-project.org/ |
| RCTD v1.2.0 | Cable et al., 2021 | https://github.com/dmcable/spacexr |
| sambamba v0.6.8 | Tarasov et al., 2015 | https://lomereiter.github.io/sambamba/index.html |
| SCANPY v1.8.2 | Wolf et al., 2018 | https://github.com/theislab/Scanpy |
| SCENIC/pyscenic v0.11.2 | Aibar et al., 2017 | https://github.com/aertslab/pySCENIC |
| Scrublet v0.2.1 | Wolock et al., 2019 | https://github.com/swolock/scrublet |
| scuttle v1.4.0 | McCarthy et al., 2017 | https://bioconductor.org/packages/scuttle/ |
| scVelo v0.2.4 | Bergen et al., 2020 | https://scvelo.readthedocs.io/ |
| Seq-n-slide | Dolgalev, 2022 | https://github.com/igordot/sns |
| Seurat v4.1.0 | Stuart et al., 2019 | https://github.com/satijalab/seurat/ |
| SingleR v1.8.0 | Aran et al., 2019 | https://github.com/dviraran/SingleR |
| singscore v4.0.3 | Foroutan et al., 2018 | https://CRAN.R-project.org/package=devtools |
| squidpy v1.1.2 | Palla et al., 2022 | https://github.com/theislab/squidpy |
| STACAS v1.1.0 | Andreatta and Carmona, 2021 | https://github.com/carmonalab/STACAS |
| STAR v2.7.3a | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| TOBIAS v0.13.2 | Bentsen et al., 2020 | https://doi.org/10.1038/s41467-020-18035-1 |
| Trimmomatic v0.36 | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| tximport v1.22.0 | Soneson et al., 2015 | https://github.com/mikelove/tximport |
| velocyto v0.17 | La Manno et al., 2018 | http://velocyto.org/ |
| VIPER v1.26.0 | Alvarez et al., 2016; Ding et al., 2018 | https://doi.org/10.1038/ng.3593 |
| Other | ||
| Original code generated in this study | This study | https://github.com/IzarLab/Melanoma_Brain_Metastasis |
| Bond RX Fully Automated Research Stainer | Leica | Cat# 21.2821 |
| Chromium Controller | 10x genomics | Cat# 120270 |
| Evos FL Auto 2 microscope | Thermo Fisher Scientific | Cat# AMAFD2000 |
| Facs Aria II | BD Biosciences | N/A |
| HiSeq 4000 | Illumina | N/A |
| Leica AT2 | Leica | N/A |
| Leica CM1950 | Leica | N/A |
| Neubauer counting chambers | Bulldog Bio | Cat# DHC-N01 |
| NovaSeq 6000 | Illumina | N/A |
| PhenoImager HT | Akoya Biosciences | https://www.akoyabio.com/phenoimager/instruments/phenoimager-ht/ |
| Qubit Flex Fluorometer | Thermo Fisher Scientific | Q33327 |
| Synergy H1 Hybrid Reader | Agilent Biotek | N/A |
| TapeStation 2200 | Agilent | N/A |
| Vevo 770 Ultrasound Imaging System | Visualsonics | N/A |
| Zeiss Celldiscoverer 7 | Zeiss | N/A |