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. Author manuscript; available in PMC: 2024 Jan 9.
Published in final edited form as: Curr Biol. 2022 Dec 16;33(1):86–97.e10. doi: 10.1016/j.cub.2022.11.042

Key Resources Table

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
TA99/Mel-5 American Type Culture Collection HB-8704
Alexafluor 488-labeled donkey anti-mouse IgG Jackson Immunoresearch 715-545-151
Bacterial and virus strains
E.coli-Top10 Invitrogen C66411
Biological samples
U. arctos- DNA sample This study GYE906
U. arctos- DNA sample This study GYE922
U. arctos- DNA sample This study GYE953
U. arctos- DNA sample This study AK17500
U. arctos- DNA sample This study AK17512
U. arctos- DNA sample This study AK17578
U. arctos- DNA sample 34 RF01
U. arctos- DNA sample 34 SJS01
U. arctos- DNA sample 34 OFS01
U. arctos- DNA sample 35 ALP1
U. arctos- DNA sample 36 AKAdmiralty1
U. arctos- DNA sample 37 AKAdmiralty2
U. arctos- DNA sample 36 AKAdmiralty3
U. arctos- DNA sample 37 AKBaranof1
U. arctos- DNA sample 34 AKBaranof2
U. arctos- DNA sample 34 AKChichagof1
U. arctos- DNA sample 34 AKChichagof2
U. arctos- DNA sample 34 AKChichagof3
U. arctos- DNA sample 34 AKChichagof4
U. arctos- DNA sample 38 AKChichagof5
U. arctos- DNA sample 36 AKDenali1
U. arctos- DNA sample 37 AKKenai
U. arctos- DNA sample 35 APN2
U. arctos- DNA sample 35 GRE2
U. arctos- DNA sample 39 JPHc1
U. arctos- DNA sample 39 JPHc2
U. arctos- DNA sample 39 JPHe1
U. arctos- DNA sample 39 JPHe2
U. arctos- DNA sample 39 JPHs1
U. arctos- DNA sample 39 JPHs2
U. arctos- DNA sample 34 MTgnp
U. arctos- DNA sample 38 Dalarna, SWE
U. maritimus- DNA sample 37 PB1
U. maritimus- DNA sample 37 PB2
U. americanus- DNA sample This study AK17023
U. americanus- DNA sample This study AK17047
U. americanus- DNA sample This study AK17117
U. americanus- DNA sample This study AZ12
U. americanus- DNA sample This study ID10
U. americanus- DNA sample This study MI334
U. americanus- DNA sample This study MI335
U. americanus- DNA sample This study MN_6083
U. americanus- DNA sample This study MS3783
U. americanus- DNA sample This study NC00417
U. americanus- DNA sample This study NC056
U. americanus- DNA sample This study NVb83
U. americanus- DNA sample This study NVb99
U. americanus- DNA sample This study NVg5
U. americanus- DNA sample This study WV17_01
U. americanus- DNA sample This study HA1
U. americanus- DNA sample This study HA2
U. americanus- DNA sample This study HA3
U. americanus- DNA sample This study HA4
U. americanus- DNA sample This study HA5
U. americanus- DNA sample This study HA6
U. americanus- DNA sample This study HA7
U. americanus- DNA sample This study HA8
U. americanus- DNA sample This study HA9
Chemicals, peptides, and recombinant proteins
BamHI NEB R0136L
HindIII NEB R0104L
XholI NEB R0146L
SnaBI NEB R0130S
Lipofectamine 2000 Invitrogen 11668-019
Hygromycin B Research Products International H75020-1.0
RPMI 1640 medium Gibco 11875-085
FBS R&D Systems S1150
PBS Corning 21-031-CM
Tris-HCl Fisher BP153-1
EDTA Sigma E5134-50G
diothiothreitol Sigma 3483-12-3
DMSO Sigma D2660
LB Broth Fisher BP1426-2
Ampicillin Fisher BP1760-25
Agar Fisher BP1423-2
Agarose GibcoBRL 15510-027
2-log DNA Ladder NEB N3200L
GelGreen Nucleic Acid Stain Biotium 41005
Tris-EDTA pH 8.0 Ambion AM9858
Terrific Broth Amresco J869-5KG
Glucose Sigma G7528-250G
Sodium Hydroxide Sigma S8045
SDS Invitrogen 15525-017
Potassium Acetate Sigma P1190-100G
Glacial Acetic Acid Fisher BP1185-500
Critical commercial assays
Prime Time Gene Expression (for qPCR) Integrated DNA Technologies (IDT) 10007065
cOmplete Protease Inhibitor Cocktail Tablets Roche P8849
Prolong Gold Antifade Mountant InVitrogen P36931
Q5 High-Fidelity DNA Polymerase NEB M0491L
QIAquick Gel Extraction Kit Qiagen 28704
BCA Protein Assay Kit Pierce 23225
Deposited data
DNA Sequencing This study SRA: PRJNA867575
TYRP1 mouse WT sequence 40 NM_031202.3
Crystal structure of the human TYRP1 luminal domain NCBI Protein Data Base 5M8L
Experimental models: Cell lines
melan-b Dorothy Bennett’s laboratory 41
Experimental models: Organisms/strains
Oligonucleotides
pBMN vector R153C primer; forward: GGGCCCTGGATATGGCAAAGTGCACAACTCACCCTTTATTTGT IDT custom oligo synthesis
pBMN vector R153C primer; reverse: ACAAATAAAGGGTGAGTTGTGCACTTTGCCATATCCAGGGCCC IDT custom oligo synthesis
pBMN vector R114C primer; forward: GACACAACTGTGGGACGTGCTGTCCTGGCTGGAGAGGAGCTGC IDT custom oligo synthesis
pBMN vector R114C primer; reverse: GCAGCTCCTCTCCAGCCAGGACAGCACGTCCCACAGTTGTGTC IDT custom oligo synthesis
pBMN flanking primer; forward: CCTCTAGACTGCCGGATCCATTTAAATTCGAATTCCTGCAGG IDT custom oligo synthesis
pBMN flanking primer; reverse: GGAATCAAAGTTGCTTCTGGATCCCATCAAGTCATCCGTGCAG IDT custom oligo synthesis
qPCR TYRP1 primer; forward: CCTTGAAGTCAGGAGAAACC This paper n/a
qPCR TYRP1 primer; reverse: CTGGTCGCAATGACAAAC This paper n/a
pPCR TYRP1 reference allele probe: FAM-ATGGCGAAGCGCACAATTC-BGQ1 This paper n/a
pPCR TYRP1 alternative allele probe: TET-ATGGCGAAGTGCACAAT-BHQ1 This paper n/a
Recombinant DNA
pCDNA3-TRP1 Gift from Walter Storkus, Univ. of Pittsburgh n/a
pBMN-I-hygro-mCherry-hSTX13 Marks laboratory 42
pBMN-I-hygro Gift from Andrew Peden, Univ. of Scheffield 43
Software and algorithms
BWA v0.7.17 44 https://github.com/lh3/bwa
GATK v4.1.8.0 45 https://gatk.broadinstitute.org/hc/en-us
SAMTOOLS v1.9 46 https://sourceforge.net/projects/samtools/files/samtools/1.9/
BCFTOOLS v1.9 47 https://sourceforge.net/projects/samtools/files/samtools/1.9/
BEAGLE v5.1 48 https://faculty.washington.edu/browning/beagle/b5_1.html
GLIMPSE 1.0.0 11 https://github.com/odelaneau/GLIMPSE/pkgs/container/GLIMPSE%2Fglimpse
GEMMA v0.98.1 12 https://github.com/genetics-statistics/GEMMA
HAPLOVIEW 4.2 14 https://www.broadinstitute.org/haploview/downloads
Haplostrips 13 https://bitbucket.org/dmarnetto/haplostrips/src/master/
PROVEAN 49 https://www.jcvi.org/research/provean#downloads
PolyPhen2 50 http://genetics.bwh.harvard.edu/pph2/
SIFT 51 https://sift.bii.a-star.edu.sg/index.html
GENEIOUSPRIME 52 https://www.geneious.com/prime/
Leica LAS-X Leica Microsystems https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/
Microvolution Bio-Vision Technologies NA
FIJI - ImageJ 53 https://imagej.net/software/fiji/
Adobe Photoshop v. 24.0.0 Adobe.com https://www.adobe.com/products/photoshop/
Graphpad Prism v. 9.4.1 GraphPad.com https://www.graphpad.com/updates/prism-900-release-notes
Pymol Schrödinger LLC https://pymol.org
program R v4.0.3 54 https://www.r-project.org/
runtc 25 https://github.com/jaredgk/runtc
STACKS v2.53 55 https://catchenlab.life.illinois.edu/stacks/
PLINK v1.9 56 https://www.cog-genomics.org/plink/
MSMC2 57 https://github.com/stschiff/msmc2
SNPable 58 https://lh3lh3.users.sourceforge.net/snpable.shtml
rangeexpansion 59 https://github.com/BenjaminPeter/rangeexpansion
selscan v2 60 https://github.com/szpiech/selscan
BayEnv2 29 https://bitbucket.org/tguenther/bayenv2_public/src/master/
PGDSpider 61 http://www.cmpg.unibe.ch/software/PGDSpider/
SLiM v3 62 https://messerlab.org/slim/
MSMC-IM 26 https://github.com/wangke16/MSMC-IM
Unipro UGENE v39.0 63 http://ugene.net/
Other
Matrigel Corning 354248
Electroporator Bio-Rad MicroPulser
PCR Bio-Rad Thermal Cycler T100
Petri Dish VWR 25384-088
Sanger Sequencing Molecular Cloning Laboratories (MCLAB) service
Mouse Tyrp1 WT,R114C and R153C synthesis and cloning Synbio Technologies custom gene synthesis
Transilluminator Clare Chemical Research Dark Reader