|
Antibodies
|
| Mouse monoclonal anti-TRP2/DCT |
Santa Cruz Biotechnology |
Cat#sc-74439; RRID:AB_1130818 |
| Mouse monoclonal anti-SOX10 |
Santa Cruz Biotechnology |
Cat# sc-365692; RRID:AB_10844002 |
| Mouse monoclonal anti-MITF |
Leica Biosystems |
Cat# NCL-L-MITF; RRID:AB_564111 |
| Mouse monoclonal anti-Ki67 |
Leica Biosystems |
Cat# KI67-MM1-CE; RRID:AB_563841 |
| Rabbit polyclonal anti-S100 |
DAKO |
Cat# Z031129-2; RRID:AB_2315306 |
| Mouse monoclonal anti-HMB45 |
DAKO |
Cat# M0634; RRID:AB_2335682 |
| Rabbit monoclonal anti-Phospho-p44/42 MAPK |
Cell Signaling Technology |
Cat# 4370; RRID:AB_2315112 |
| Rabbit monoclonal anti-Phospho-MEK1/2 (Ser221) (166F8) |
Cell Signaling Technology |
Cat# 2338; RRID:AB_490903 |
| Mouse monoclonal anti-PCNA |
Cell Signaling Technology |
Cat# 2586; RRID:AB_2160343 |
| Rabbit monoclonal anti-CD8 |
Cell Signaling Technology |
Cat# 98941; RRID:AB_2756376 |
| Rabbit polyclonal anti-CD163 |
Biorbyt |
Cat# orb13303; RRID:AB_10749283 |
| Mouse monoclonal anti-CD161 |
Novus Biologicals |
Cat# NBP2-14844; RRID: N/A |
| Rabbit polyclonal anti-NRASQ61R
|
Abcam |
Cat# ab227658; RRID: N/A |
| Mouse monoclonal anti-p16INK4A
|
Abcam |
Cat# ab54210; RRID:AB_881819 |
| Rabbit monoclonal anti-MelanA |
Abcam |
Cat #ab210546; RRID:AB_2889292 |
| Hamster monoclonal anti-CD11c |
Abcam |
Cat# ab33483; RRID:AB_726084 |
| Rat monoclonal anti-CD3 |
Abcam |
Cat# ab11089; RRID:AB_2889189 |
| Rabbit monoclonal anti-CD4 |
Abcam |
Cat# ab183685; RRID:AB_2686917 |
| Rat monoclonal InVivoMAb anti-mouse CD4 |
BioXCell |
Cat# BE0003-1; RRID:AB_1107636 |
| Rat monoclonal InVivoMAb anti-mouse CD8α |
BioXCell |
Cat# BE0061; RRID:AB_1125541 |
| Rat monoclonal InVivoMAb rat IgG2b isotype control, anti-keyhole limpet hemocyanin |
BioXCell |
Cat# BE0090; RRID:AB_1107780 |
| Rat monoclonal InVivoMab anti-mouse F4/80 |
BioXCell |
Cat# BE0206; RRID:AB_10949019 |
| Rabbit polyclonal anti-TRP2 |
Abcam |
Cat# ab74073; RRID:AB_1524517 |
| Rat monoclonal anti-F4/80 |
Abcam |
Cat# ab16911; RRID:AB_443548 |
| Goat polyclonal Alexa Fluor 488-AffiniPure Anti-Rabbit IgG (H+L) |
Jackson ImmunoResearch Labs |
Cat# 111-545-144; RRID:AB_2338052 |
| Donkey polyclonal Alexa Fluor® 594 AffiniPure Anti-Rabbit IgG (H+L) |
Jackson ImmunoResearch Labs |
Cat# 711-585-152; RRID:AB_2340621 |
| Rabbit monoclonal anti-SOX10 |
Abcam |
Cat# ab155279; RRID:AB_2650603 |
| Mouse monoclonal anti-HMB-45 |
Abcam |
Cat# ab732; RRID:AB_305844 |
|
|
|
|
Bacterial and Viral Strains
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Biological samples
|
|
|
| De-identified nevus tissue |
Mass General Brigham Healthcare |
IRB Protocol 2017P000992 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Chemicals, peptides, and recombinant proteins
|
| 4-hydroxytamoxifen |
Sigma-Aldrich |
Cat#H6278; CAS: 68392-35-8 |
| Binimetinib (MEK162) |
Selleckchem |
Cat#S7007; CAS 606143-89-9 |
| Trametinib (GSK1120212) |
Selleckchem |
Cat# S2673; CAS 871700-17-3 |
| Omipalisib (GSK2126458) |
Selleckchem |
Cat# S2658; CAS 1086062-66-9 |
| Imatinib (STI571) |
Selleckchem |
Cat# S2475; CAS 152459-95-5 |
| Squaric acid dibutylester (SADBE) |
Sigma-Aldrich |
Cat# 339792; CAS 2892-62-8 |
| 16% Paraformaldehyde Aqueous Solution, EM Grade, Ampoule 10 ML |
Electron Microscopy Sciences |
Cat# 50-980-487 |
| Hematoxylin 2 |
Epredia |
Cat# 7231 |
| Nuclear Fast Red |
Abcam |
Cat #ab246831 |
| RNAlater |
Life Technologies |
Cat# AM7020 |
| EQUISUL-SDT® (SULFADIAZINE/TRIMETHOPRIM) |
Aurora Pharmaceuticals |
Cat# SC-395895Rx |
| Citrate Buffer (pH 6.0), Concentrate |
Life Technologies |
Cat# 005000 |
| Goat Serum |
Sigma Aldrich |
Cat# G9023 |
| DAPI |
Sigma Aldrich |
Cat# D9542; CAS:28718-90-3 |
| Fluoromount G |
Southern Biotech |
Cat# 0100-01 |
|
Critical commercial assays
|
| RNeasy Plus Universal Kit |
Qiagen |
Cat# 73404 |
| Agilent RNA 6000 Nano Kit |
Agilent Technologies |
Cat# G2938-90034 |
| Fontana-Masson Stain Kit (Melanin Stain) |
Abcam |
Cat# ab150669 |
| RNA FFPE Miniprep kit |
Zymo Research |
Cat# R1009 |
| Agilent RNA 6000 Pico Kit |
Agilent Technologies |
Cat# G2938-90046 |
| Quant-it™ RiboGreen RNA Assay Kit and RiboGreen RNA Reagent |
ThermoFisher Scientific |
Cat# R11490
|
| Illumina Ribo-Zero Plus rRNA Depletion Kit |
Illumina |
Cat# 20037135 |
| QIAamp DNA FFPE Tissue Kit |
Qiagen |
Cat# 56404 |
| High Sensitivity RNA ScreenTape Analysis |
Agilent Technologies |
Cat# 5067-5579 |
| Illumina® Stranded mRNA Prep, Ligation (96 Samples) |
Ilumina |
Cat# 20040534 |
| Deposited data / Publicly available data |
| Raw and analyzed CMN Model RNA Seq Data |
This Paper |
GEO: |
| Raw and analyzed DCT SADBE RNA Seq Data |
This Paper |
GEO: |
| LM22 (leukocyte gene signature matrix) |
Stanford University CIBERSORT |
Newman et al. 2015
|
|
|
|
|
|
|
|
Experimental models: Cell lines
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Experimental models: Organisms/strains
|
| Mouse: Lox-stop-Lox (LSL)-NrasQ61R: C57Bl/6 Nrastm1.1Nesh
|
Burd et al., 2014 Sourced from Drs. Christin Burd and Norman Sharpless, University of North Carolina |
MGI:5645358 |
| Mouse: Dct-Cre: C57BL/6 Dcttm1(Cre)Bee
|
Guyonneau et al., 2004 Sourced from Dr. Friedrich Beermann, ISREC, Lausanne, Switzerland |
MGI:2387116 |
| Mouse: Tyr-Cre: C57BL/6 Tg(Tyr-cre)1Lru |
Delmas et al., 2003 Source from Dr. Lionel Larue, Institut Curie, Paris, France |
MGI:3573939 |
| Mouse: Tyr-CreERT2: C57B1/6 Tg(Tyr-cre/ERT2)13Bos |
Bosenberg et al., 2006 Sourced from Dr. Marcus Bosenberg, Yale University |
MGI:3641203 |
| Mouse:SHO: Crl:SHO-PrkdcscidHrhr
|
Charles River Laboratories |
RRID: IMSR_CRL:474 |
|
|
|
| Oligonucleotides |
| Primer DCT Forward: TTGAGAGGAGAGGAAAGGGC |
Guyonneau et al., 2004
|
N/A |
| Primer DCT Reverse: CACGCCATCCAAGGTCATGC |
Guyonneau et al., 2004
|
N/A |
| Primer CRE Reverse: CATTGCTGTCACTTGGTCGT |
Guyonneau et al., 2004
|
N/A |
| Primer NRAS Q61R: GCAAGAGGCCCGGCAGTACCTA |
Burd et al., 2014
|
N/A |
| Primer NRAS 1: AGACGCGGAGACTTGGCGAGC |
Burd et al., 2014
|
N/A |
| Primer NRAS 2: GCTGGATCGTCAAGGCGCTTTTCC |
Burd et al., 2014
|
N/A |
| Primer Tyr::CRE<ERT2> 1: CAGGGTGTTATAAGCAATCCC |
Bosenberg et al., 2006
|
N/A |
| Primer Tyr::CRE<ERT2> 2: CCTGGAAAATGCTTCTGTCCG |
Bosenberg et al., 2006
|
N/A |
| Primer Tyr::CRE Forward: GTCACTCCAGGGGTTGCTGG |
Delmas et al., 2003
|
N/A |
| Primer Tyr::CRE Reverse: CCGCCGCATAACCAGTGA |
Delmas et al., 2003
|
N/A |
| Recombinant DNA |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Software and algorithms |
| GraphPad Random Treatment Assigner |
GraphPad |
https://www.graphpad.com/quickcalcs/randomize1/
|
| Zeiss Zen Image Software, Version 2.3 |
Zeiss |
https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html
|
| ImageJ |
National Institutes of Health (NIH) |
https://imagej.nih.gov/ij/
|
| NIS Elements imaging software |
Nikon Instruments Inc |
https://www.microscope.healthcare.nikon.com/products/software/nis-elements
|
| DESeq2 |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Prism 7 |
Graphpad |
https://www.graphpad.com/support/prism-7-updates/
|
| DRAGEN FastQC |
Illumina |
https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/FASTQC_Intro_fDG.htm
|
| Salmon v 1.8.0 |
Patro et al., 2017
|
https://github.com/COMBINE-lab/Salmon
|
| NDP.view2 v 2.8.24 |
Hamamatsu |
https://www.hamamatsu.com/us/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html
|
| R package: fgsea |
Korotkevich et al., 2021
|
https://doi.org/10.1101/060012
|
| R package: clusterProfiler |
Yu et al., 2012
|
https://doi.org/10.1089/omi.2011.0118
|
| Other |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
