o propargyl puromycin opp  (Jena Bioscience)


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    Name:
    O Propargyl puromycin
    Description:

    Catalog Number:
    NU-931-05
    Price:
    146.36
    Category:
    Nucleotides Nucleosides
    Size:
    0 5 mg
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    Structured Review

    Jena Bioscience o propargyl puromycin opp
    Downregulation of protein synthesis in <t>T-IEL</t> (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin <t>(OPP)</t> incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)

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    Images

    1) Product Images from "Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes"

    Article Title: Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes

    Journal: bioRxiv

    doi: 10.1101/2021.03.15.435419

    Downregulation of protein synthesis in T-IEL (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin (OPP) incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)
    Figure Legend Snippet: Downregulation of protein synthesis in T-IEL (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin (OPP) incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)

    Techniques Used: Expressing, Ex Vivo, Negative Control, Flow Cytometry, Derivative Assay

    Related Articles

    Imaging:

    Article Title: Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells.
    Article Snippet: Briefly, HSC were cultured in medium 548 supplemented with LysoBriteGreen (AAT Bioquest, Cat No 22643), anti-CD71-PE and imaged 549 continuously on 10 µg/mL anti-CD43 coated IBIDIVI 0.4 channel slide (Ibidi). .. After time-lapse 550 imaging 44 h of in vitro culture medium was exchanged and cells were incubated for 1 h at 37 °C 551 and 5% CO2 in medium supplemented with 50 µM O-propargyl-Puromycin (Jena Bioscience). .. 552 Afterwards cells were fixated with 4% para-formaldehyde, permeabilized, blocked and cross-553 linked for 30min using the Click-iT reaction buffers and 250 nM AlexaFluor-647-azide (Thermo 554 Fisher).

    In Vitro:

    Article Title: Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells.
    Article Snippet: Briefly, HSC were cultured in medium 548 supplemented with LysoBriteGreen (AAT Bioquest, Cat No 22643), anti-CD71-PE and imaged 549 continuously on 10 µg/mL anti-CD43 coated IBIDIVI 0.4 channel slide (Ibidi). .. After time-lapse 550 imaging 44 h of in vitro culture medium was exchanged and cells were incubated for 1 h at 37 °C 551 and 5% CO2 in medium supplemented with 50 µM O-propargyl-Puromycin (Jena Bioscience). .. 552 Afterwards cells were fixated with 4% para-formaldehyde, permeabilized, blocked and cross-553 linked for 30min using the Click-iT reaction buffers and 250 nM AlexaFluor-647-azide (Thermo 554 Fisher).

    Incubation:

    Article Title: Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells.
    Article Snippet: Briefly, HSC were cultured in medium 548 supplemented with LysoBriteGreen (AAT Bioquest, Cat No 22643), anti-CD71-PE and imaged 549 continuously on 10 µg/mL anti-CD43 coated IBIDIVI 0.4 channel slide (Ibidi). .. After time-lapse 550 imaging 44 h of in vitro culture medium was exchanged and cells were incubated for 1 h at 37 °C 551 and 5% CO2 in medium supplemented with 50 µM O-propargyl-Puromycin (Jena Bioscience). .. 552 Afterwards cells were fixated with 4% para-formaldehyde, permeabilized, blocked and cross-553 linked for 30min using the Click-iT reaction buffers and 250 nM AlexaFluor-647-azide (Thermo 554 Fisher).

    Article Title: An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function
    Article Snippet: .. O‐Propargyl‐puromycin labeling of nascent peptides Cells were incubated with 25 μM O‐propargyl‐puromycin (Jena Bioscience) for indicated time at 43°C and fixed using 4% PFA in PBS. ..

    Flow Cytometry:

    Article Title: Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
    Article Snippet: After washing the immunoprecipitated, they were treated with proteinase K. RNA extraction was performed by the phenol–chloroform method, and 200–500 ng of purified RNA was converted to cDNA using the Verso cDNA kit (Thermo Scientific). qPCR was used to validate target mRNAs bound by MSI2 and control cells. .. O -Propargyl-Puromycin incorporation by flow cytometry Cells were plated at a density of 200,000 cells mL−1 and pre-treated with DMSO or Ro up to 4 h. Then, 50 μM O -propargyl-puromycin (OP-Puro; NU-931–05, Jena Bioscience) was added. .. Control cells were co-incubated with DMSO or Ro and treated with 150 μg mL-1 cycloheximide for 15 min. Non-OP-Puro treated cells were also used as negative controls for flow cytometry.

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Chromatin Immunoprecipitation:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Polymerase Chain Reaction:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Transfection:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Gel Extraction:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    RNA Sequencing Assay:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Microarray:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Polyacrylamide Gel Electrophoresis:

    Article Title: Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
    Article Snippet: BA1 cells from: Wnt1::Cre;Yy1fl/wt; Wnt1::Cre;Yy1fl/fl; Wnt1::Cre;Yy1wt/wt This paper N/A Chemicals, Peptides, and Recombinant Proteins FCS Thermo Fischer Scientific Cat# 16140 L-glutamine Thermo Fischer Scientific Cat# 25030 Tamoxifen Sigma-Aldrich Cat# T5648; CAS# 10540-29-1 Isoflurane Piramal Healthcare Cat# 430024079 Fibronectin Sigma-Aldrich Cat# F11141 Human Recombinant TGFb1 PrepoTech Cat# 100-21 Human Recombinant BMP2 PrepoTech Cat# 120-02 Human Recombinant Neuregulin Type I PrepoTech Cat#100-03 Fibronectin Sigma-Aldrich Cat# F6886; CAS# 66575-29-9 HBSS (no Calcium or Magnesium) Thermo Fischer Scientific Cat# 14170 Collagenase Type 3 Worthington Cat# M3D14157 Trypsin Thermo Fischer Scientific Cat# 25200 B27 Supplement Thermo Fischer Scientific Cat# 12587-010 N2 Supplement Thermo Fischer Scientific Cat# 17502-048 FGF2 R Systems Cat# 233-FB-001MG/CF CHIR 99021 Tocris Cat# 44230 Liberase DH Research Grade Roche Cat# 0.5401054001 DNAase I Roche Cat# 10104159001 RLT Buffer QIAGEN Cat# 79216 Bouin’s Fixative Sigma-Aldrich Cat# HT101128 Ammonium Hydroxide Sigma-Aldrich Cat# 338818; CAS#1336-21-6 Alcian Blue Sigma-Aldrich Cat# A5268; CAS# 33864-99-2 Acetic Acid Sigma-Aldrich Cat# A6283; CAS# 64-19-7 Benzyl Alcohol Sigma-Aldrich Cat# 305197; CAS# 100-51-6 Benzyl Benzoate Sigma-Aldrich Cat# B6630; CAS# 120-51-4 O.C.T Compound Scigen Cat# AGR1180 Roti-Histofix Carl Roth Cat# P087.3 Tween-20 Sigma-Aldrich Cat# P1379; CAS# 9005-64-5 Blocking Reagent Perkin-Elmer Cat# FP1020 Hoeschst 33342 Sigma-Aldrich Cat# 14533; CAS# 23491-52-3 Fluorescent Mounting Medium Dako Cat# S3023 EdU Thermo Fischer Scientific Cat# C10424 RIPA Buffer Thermo Fischer Scientific Cat# 89900 Protease Inhibitor Thermo Fischer Scientific Cat# 87786 Phosphatase Inhibitor Thermo Fischer Scientific Cat# 78420 Odyssey Blocking Buffer Li-COR Biosciences Odyssey blocking buffer SYBR Green I Master Mix Roche Cat# 4707516001 Non-buffered XF Base DMEM Minimal Medium Agilent Cat# 103334 (Continued on next page) Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 e2 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligomycin Agilent Cat# 103015-100 Acetonitrile Sigma-Aldrich Cat# 271004; CAS# 75-05-8 Uridine Sigma-Aldrich Cat# U3003; CAS# 58-96-8 Glutamic Acid Dimethyl Ester Sigma-Aldrich Cat# 49560; CAS# 23150-65-4 L-aspartic Acid Dimethyl Ester Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 L-Carnitine Hydrochloride Sigma-Aldrich Cat# 456233; CAS# 32213-95-9 Nucleoside Mix Millipore Cat# ES-008-D OP-Puro Jena Bioscience Cat# Nu-931-5 PI/RNase Solution Invitrogen Cat# F10797 Polybrene Sigma-Aldrich Cat# H9268; CAS# 28728-55-4 FCCP Agilent Cat# 103015-100 Antimycin/Rotenone Agilent Cat# 103015-100 Dispase I Roche Cat# 04942086001 Critical Commercial Assays Annexin V Apoptosis Detection Kit BD PharMingen Cat# 556547 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fischer Scientific Cat# C10424 TSA Plus Cyanine System Perkin-Elmer Cat# NEL744001 Maxima First Strand cDNA Synthesis kit Thermo Fischer Scientific Cat# K1641 Magna ChIP A/G kit Millipore Cat# 17-10085/86 Seahorse Mito Stress Test kit Agilent Cat# 103015-100 High Fidelity PCR Master Kit Roche Cat# 2140314001 Anza T4 DNA Ligase Master Mix Thermo Fischer Scientific Cat# IVGN2108 Gateway LR Clonase II mix Thermo Fischer Scientific Cat# 11791020 Click-IT Protein Synthesis Assay Kit Thermo Fischer Scientific Cat# C10458 Jet Prime Transfection Reagent Polyplus Cat# 114-75 RNAeasy Mini Kit QIAGEN Cat# 74106 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 Deposited Data RNa-seq in Control and Yy1 cko BA1 cells This paper PRJEB21547 RNA-seq in Si-Control and Si-YY1 human melanoma cells This paper PRJEB21636 YY1 ChIP seq This paper PRJEB21646 MITF ChiP seq (Strub et al., 2011) GSM1565011 SOX10 ChIP seq (Laurette et al., 2015) GSM1517752 RNA-seq in wild-type melanocytes and NrasQ61K;Cdkn2a / melanocytes This paper PRJEB30285 Microarray in NCSCs and their primed counterparts This paper GEO: GSE125480 Experimental Models: Cell Lines Human Melanoma: M010817 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M050829 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M980513 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M000921 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: M130429 URPP Live Cell Biobank, University of Zurich N/A Human Melanoma: Skmel28 ATCC Cat# HBT-72 Human Melanoma: A375 ATCC Cat# CRL-1619 Human Melanoma: Mel888 (Rubinfeld et al., 1997) N/A (Continued on next page) e3 Cell Stem Cell 24, 637–653.e1–e9, April 4, 2019 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human Prostate Cancer: PC3 ATCC Cat# CRL-1435 Human Prostate Cancer: Du145 ATCC Cat# HTB-81 Human Breast Cancer: MDA-MB-231 ATCC Cat# HTB26 Human Breast Cancer: T47-D ATCC Cat# HBT-133 Human Colon Cancer: WIDr ATCC Cat# CCL-218 Human Adrenal Carcinoma: NCI-H295R ATCC Cat# CRL-2128 HEK293T ATCC Cat# CRL-1573 Experimental Models: Organisms/Strains Mouse Wnt1::Cre: H2afvTg(Wnt1-cre)11Rth (Danielian et al., 1998) MGI: 2386570 Mouse Sox10::CreERT2: Tg(Sox10-icre/ERT2)1Ldim (Simon et al., 2012) N/A Mouse: Hsd:Athymic Nude-Foxn1nu/nu Envigo N/A Mouse: Tyr::CreERT2: B6.Cg-Tg(Tyr-cre/ERT2)13Bos/J The Jackson Laboratory Cat# 012328; RRID: IMSR_JAX:012328 Mouse: R26R-LSL-tdTomato: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J The Jackson Laboratory Cat# 007914; RRID: IMSR_JAX:007914 Mouse:Yy1fl/fl: B6;129S4-Yy1tm2Yshi/J The Jackson Laboratory Cat# 014649; RRID:IMSR_JAX:014649 Mouse: R26R-EGFP: Gt(ROSA)26Sortm1Sho The Jackson Laboratory Cat# 003504; RRID:IMSR_JAX:003504 Oligonucleotides Mouse Genotype Primers, See Table S5 Mycrosynth N/A Human qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse qRT-PCR Primers, See Table S6 Mycrosynth N/A Mouse ChiP qRT-PCR Primers, See Table S7 Mycrosynth N/A Recombinant DNA Stealth Si RNA Targeting YY1 (Si-YY1) Thermo Fischer Scientific Cat# YY1HSS111432 Stealth Medium GC Content Scrambled Si RNA (Si-Control) Thermo Fischer Scientific Cat# 12935 pCDH-Puro-cMYC Addgene Cat# 46970 pMuLE-ENTR-CMV-L1-R5 Vector Addgene (Albers et al., 2015) Cat# 62090 pMuLE-ENTR-SV40-eGFP-L5-L2 Addgene (Albers et al., 2015) Cat# 62144 pLenti-X1-Piro-DEST Addgene (Albers et al., 2015) Cat# 11297 Software and Algorithms UCSC Genome Browser https://genome.uscs.edu/ N/A Human Metabolome Database v3.0 http://www.hmdb.ca/ N/A Small Molecule Pathway Database http://smpdb.ca/ N/A MACS Software http://liulab.dfci.harvard.edu/MACS/ N/A SeqMINER http://bips.u-strasbg.fr/seqminer/ N/A ISMARA https://ismara.unibas.ch /mara N/A ClueGo v2.3.2 http://apps.cytoscape.org/ apps/cluego N/A Cytoscape v3.4.0 https://cytoscape.org N/A Graphpad Prism GraphPad N/A MATLAB https://ch.mathworks.com N/A FlowJo v7.6 Tree Star N/A Bowtie 2 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml N/A HOMER tool package http://homer.ucsd.edu/homer/ N/A

    Labeling:

    Article Title: An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function
    Article Snippet: .. O‐Propargyl‐puromycin labeling of nascent peptides Cells were incubated with 25 μM O‐propargyl‐puromycin (Jena Bioscience) for indicated time at 43°C and fixed using 4% PFA in PBS. ..

    Article Title: BAG3 and BAG6 differentially affect the dynamics of stress granules by targeting distinct subsets of defective polypeptides released from ribosomes
    Article Snippet: Cells were lysed in Laemmli buffer and subsequently processed for Western blot analysis with the indicated antibodies. .. Analysis of nascent proteins by confocal microscopy: newly synthesized proteins were labeled by incubating the cells with 25 μM O-propargyl-puromycin (OP-puro) (Jena Bioscience) for the indicated time points; where indicated, cells were co-treated with MG132 (Sigma-Aldrich) and VER-155008 (Sigma-Aldrich). ..

    Confocal Microscopy:

    Article Title: BAG3 and BAG6 differentially affect the dynamics of stress granules by targeting distinct subsets of defective polypeptides released from ribosomes
    Article Snippet: Cells were lysed in Laemmli buffer and subsequently processed for Western blot analysis with the indicated antibodies. .. Analysis of nascent proteins by confocal microscopy: newly synthesized proteins were labeled by incubating the cells with 25 μM O-propargyl-puromycin (OP-puro) (Jena Bioscience) for the indicated time points; where indicated, cells were co-treated with MG132 (Sigma-Aldrich) and VER-155008 (Sigma-Aldrich). ..

    Synthesized:

    Article Title: BAG3 and BAG6 differentially affect the dynamics of stress granules by targeting distinct subsets of defective polypeptides released from ribosomes
    Article Snippet: Cells were lysed in Laemmli buffer and subsequently processed for Western blot analysis with the indicated antibodies. .. Analysis of nascent proteins by confocal microscopy: newly synthesized proteins were labeled by incubating the cells with 25 μM O-propargyl-puromycin (OP-puro) (Jena Bioscience) for the indicated time points; where indicated, cells were co-treated with MG132 (Sigma-Aldrich) and VER-155008 (Sigma-Aldrich). ..

    Cell Culture:

    Article Title: Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes
    Article Snippet: Data were analysed using FlowJo software (TreeStar). .. OPP assayT-IEL and LN single cell suspensions were cultured with 20µM O-propargyl-puromycin (OPP) (JenaBioscience) for 15 minutes. .. As a negative control, cells were pre-treated with 0.1mg/mL cycloheximide (CHX) for 15 minutes before adding the OPP for 15 minutes (30-minute total CHX exposure).

    Injection:

    Article Title: Regulated Inositol-Requiring Enzyme 1 dependent mRNA decay sets the threshold for dendritic cell survival
    Article Snippet: In-vivo, B-I09 was injected IP at a final concentration of 0.625 mg/25g mouse. .. O-Propargyl Puromycin (NU-931-5; Jena Bioscience) was dissolved in DMSO, further diluted in PBS (10 mg/ml) and injected IP (50 mg/kg mouse weight). .. 1 hour after injection mice were euthanized by cervical dislocation and the organs of interest were collected.

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    Jena Bioscience o propargyl puromycin opp
    Downregulation of protein synthesis in <t>T-IEL</t> (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin <t>(OPP)</t> incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)
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    Downregulation of protein synthesis in T-IEL (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin (OPP) incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)

    Journal: bioRxiv

    Article Title: Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes

    doi: 10.1101/2021.03.15.435419

    Figure Lengend Snippet: Downregulation of protein synthesis in T-IEL (A) Estimated total cytoplasmic (left) and mitochondrial (right) ribosomal protein content for LN TCRβ CD8αβ T cells and all T-IEL subsets. (B) Protein expression Log2 fold change (T-IEL/LN CD8 T cells) for Polymerase 1, 2 and 3 complexes. Each grey dot represents one of the polymerase subunits. (C) Estimated protein copy numbers of the amino acid transporters, SLC7A5 and SLC38A2, for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (D) Estimated protein copy numbers of Arginase 2 (ARG2; left) and alanine aminotransferase (GPT; right) for WT LN TCRβ CD8αβ and all 3 subsets of T-IEL. (E) Estimated protein copy numbers of PRKR-Like Endoplasmic Reticulum Kinase (PERK) for WT LN TCRβ CD8αβ and all 3 T-IEL subsets. (F) OP-Puromycin (OPP) incorporation in ex vivo WT LN TCRβ CD8αβ and T-IEL. As a negative control, OPP incorporation was inhibited by cycloheximide (CHX) pre-treatment. OPP incorporation was assessed by flow cytometry 15 min after administration. Bar graph represents the geometric MFI of the OPP-AlexaFluor 647 in each T cell subsets normalized to the geometric MFI of the CHX pre-treated T cells. All error bars are SEM. Proteomic and OPP assay data are derived from at least 3 biological replicates. Symbols on the bars represent the biological replicates (except for B .)

    Article Snippet: OPP assayT-IEL and LN single cell suspensions were cultured with 20µM O-propargyl-puromycin (OPP) (JenaBioscience) for 15 minutes.

    Techniques: Expressing, Ex Vivo, Negative Control, Flow Cytometry, Derivative Assay