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    Thermo Fisher bca protein assay kit thermo fisher scientific
    Bca Protein Assay Kit Thermo Fisher Scientific, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bca+protein+assay+kit+thermo+fisher/BCA+Protein+Assay+Kit/pm42361797-227-195-199
    Average 99 stars, based on 1 article reviews
    bca protein assay kit thermo fisher scientific - by Bioz Stars, 2026-10
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    Article Title: TET3 is a regulator and can be targeted for the intervention of myocardial fibrosis.
    Article Snippet: Reagent/resource Reference or source Identifier or catalog number Ad5-CMV-3FLAG-EGFP Genechem N/A Antibodies This study Appendix Table S2 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S1 siRNA This study Appendix Table S1 Chemicals, enzymes, and other reagents Human cardiac fibroblasts Lifeline #FC-0060 Dulbecco’s modified Eagle’s medium (DMEM) Gibco #11965092 Fetal bovine serum (FBS) Gibco #10270-106 Opti-MEM Gibco #31985070 Trypsin(0.25%) Gibco #25200072 LipofectamineTM RNAiMAX Transfection reagent Invitrogen #13778150 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 594 dye Invitrogen #C10639 Bobcat339 hydrochloride Selleck #S6682 D-GsMTx4 TFA Targetmol #T37697L Collagen Type I Rat Tail Corning #354236 Corning 35 mm TC-treated Culture Dish Corning #430165 Corning 60-mm TC-treated culture dish Corning #430166 Corning 100-mm TC-treated culture dish Corning #430167 Tissue culture plate-six well Jetbiofil #TCP011006 Tissue culture plate-12 well Jetbiofil #TCP011012 Tissue culture plate-48 well Jetbiofil #TCP011024 Cell lysis buffer for Western and IP Beyotime #P0013 Penicillin-Streptomycin solution Beyotime #C0222 Hydroxyproline assay kit Solarbio #BC0250 Masson’s Trichrome Stain Kit Solarbio #G1346 Picrosirius Red Stain Kit Solarbio #G1472 Recombinant human TGF-beta 1 protein R&D #7754-BH Goat anti-rabbit IgG (H+ L) crossadsorbed secondary antibody, Alexa FluorTM 594 Thermo Fsher #A-11012 Thermo Scientific PageRuler Plus Thermo Fisher #26620 Pierce BCA Protein Assay Kit Thermo Fisher #23225 Phenylmethylsulfonyl fluoride(PMSF) Thermo Fisher #36978 Tamxifen Sigma #T5648 DMSO Sigma #D8418 Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro Vazyme #TD904-01 VAHTS DNA Clean Beads Vazyme #N411 TruePrep Index Kit V2 for Illumina Vazyme #TD202 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme #TD711 Reagent/resource Reference or source Identifier or catalog number FastPure Cell/Tissue Total RNA Isolation Kit Vazyme #RC101-01 HiScript II Q RT SuperMix for qPCR Vazyme #R222-01 ChamQ SYBR Color qPCR Master Mix Vazyme #Q411-02 Software GraphPad Prism9 GraphPad Software, Inc RRID:SCR_002798 ImageJ-Fiji https:// imagej.net/ software/fiji/ RRID:SCR_002285 Adobe Illustrator Adobe Systems RRID:SCR_010279

    Polymerase Chain Reaction:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

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    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Gel Extraction:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    RNA Extraction:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    cDNA Synthesis:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Bicinchoninic Acid Protein Assay:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Article Title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal ScRPL-3 Deposited to the DSHB by Warner, J.R DSHB Hybridoma Product ScRPL3; AB_1553774 Mouse monoclonal anti-HA Roche Cat#11867423001; AB_390918 Mouse monoclonal anti-FRQ Dr. Michael Brunner Clone 3G11-1B10-E2 Rabbit monoclonal EIF2S1 (phosphoS51) Abcam Cat#32157; AB_732117 Anti-mouse IgG-HRP Bio-Rad Cat#170-6516; AB_11125142 Anti-mouse 800 nm LiCor IR dye Li-Cor Cat#925-32210; AB_2687825 Anti-rabbit 680 nm LiCor IR dye Li-Cor Cat#926-68076; AB_10956590 Chemicals, Peptides, and Recombinant Proteins Basta, glufosinate ammonium Liberty Cat#280SL SuperSignal TM West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat#34077 SuperSignal TM West Femto Maximum Sensitivity Substrate Thermo Scientific Cat#34085 Hygromycin VWR Cat#80055-268 PMSF Sigma-Aldrich Cat#P7626 Phosphatase Inhibitor Cocktail 2 Millipore Cat#P5726 Luciferin Gold Biotechnology Cat#LUNCA-300 Sodium ortho-vanadate Sigma-Aldrich Cat#S6508 β-glycerophosphate Sigma-Aldrich Cat#G6376 Aprotinin Sigma-Aldrich Cat#A1153 Leupeptin hemisulfate salt Sigma-Aldrich Cat#L2884 Pepstatin A Sigma-Aldrich Cat#P5318 Bathocuproinedisulfonic acid (BCS) Thermo Scientific Cat#164060050 Immobilon-P PVDF membrane Millipore Cat#IPVH00010 Immobilon-FL PVDF membrane Millipore Cat# IPFL00010 Cycloheximide Sigma-Aldrich Cat#C7698-5G Turbo DNase Thermo Fisher Cat#AM2238 RNase I Thermo Fisher Cat#AM2294 CircLigase Epicentre Cat#CL4111K GlycoBlue TM Thermo Fisher Cat#AM9515 miRNeasy Mini Kit Qiagen Cat#217004 T4 RNA ligase 2 truncated New England Biolabs Cat#M0242L SuperScript TM III Reverse Transcriptase Thermo Fisher Cat#18080044 Phusion Hot Start High-Fidelity DNA Polymerase Thermo Fisher Cat#F540L DNA high-sensitivity chip Agilent Cat# 067-4626 Quant-iT TM RiboGreen RNA assay kit Thermo Fisher Cat# R11490 Oligo d(T) 25 Magnetic Beads NEB Cat#S1419S Turbo DNA-free TM Kit Ambion Cat#AM1907 Terminator 5 ′ -Phosphate-Dependent Exonuclease Lucigen Cat#TER51020 SENSE Total RNA-seq Library Preparation Kit Lexogen Cat#009 (Continued on next page) 16 Cell Reports 44, 116484, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER HEPES Sigma Cat#H4034-500G Sodium citrate, dihydrate Millipore Sigma Cat#567446 Paromomycin MP Biochemicals Cat#194535 Dual Glo TM luciferase assay kit Promega Cat#E2920 BCA Protein Assay Kit Thermo Fisher Cat23225 Acetonitrile Fisher Scientific Cat#A9554 Formic Acid Thermo Fisher Cat#28905 Deposited data Circadian intact particle mass spec on ribosomes isolated from WT cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian intact particle mass spec on ribosomes isolated from Δfrq cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian RPF-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282318: GSM8641256 thru GSM8641275 Circadian RNA-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282317: GSM8641276 thru GSM8641295 Raw Data, Mendeley This paper https://doi.org/10.17632/9xpty464cs.1 Experimental models: Organisms/strains Neurospora crassa wild type 74-OR23-IV mat a FGSC FGSC 4200; DBP 985 Neurospora crassa wild type 74-OR23-IV mat A FGSC FGSC 2489; DBP 984 Δmus-51::bar, mat a FGSC FGSC 9718;DBP 641 Δfrq::bar, mat a Bennett et al. 113 DBP 1320 Δfrq::bar, mat A Bennett et al. 113 DBP 1228 Δel-31(ncu08344):hph, mat a This paper DBP 3602 Δel-31(ncu08344):hph, mat A This paper DBP 3274 Complemented Δel-31::hph, Ec el-31 WT , Ec bar + This paper DBP 3585 ras-1 bd , Δel-31::hph, mat A This paper DBP 3280 ras-1 bd , mat A This paper DBP 1582 Δssz-1(ncu00692)::hph FGSC FGSC 14067; DBP 3478 eif-4g::luc translational fusion This paper DBP 4847-4849 Δfrq::bar, eif-4g::luc translational fusion This paper DBP 4850-4853 rrp-15::luc translational fusion This paper DBP 4854-4856 Δfrq::bar, rrp-15::luc translational fusion This paper DBP 4857-4860 ssf-1::luc translational fusion This paper DBP 4775-4776 Δfrq::bar, ssf-1::luc translational fusion This paper DBP 4778, 4779, 4781 gol-9::luc translation fusion This paper DBP 4726 (sib to DBP 4730) or DBP 4735 (sib to DBP4734) Δfrq::bar, gol-9::fluc translation fusion This paper DBP 4730 Δel-31::hph gol-9::fluc translation fusion This paper DBP 4734 tcf-14::luc translation fusion This paper DBP 4302 (sib to DBP 4305) or DBP 4349 (sib to DBP 4354) Δfrq::bar, tcf-14::fluc translation fusion This paper DBP 4305 Δel-31::hph tcf-14::fluc translation fusion This paper DBP 4354 ens-3::fluc translation fusion This paper DBP 4310 (sib to DBP 4312) or DBP 4357 (sib to DBP 4362) (Continued on next page) Cell Reports 44, 116484, November 25, 2025 17 ..

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Multiplex Assay:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Chromatin Immunoprecipitation:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    RNA Sequencing:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Article Title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal ScRPL-3 Deposited to the DSHB by Warner, J.R DSHB Hybridoma Product ScRPL3; AB_1553774 Mouse monoclonal anti-HA Roche Cat#11867423001; AB_390918 Mouse monoclonal anti-FRQ Dr. Michael Brunner Clone 3G11-1B10-E2 Rabbit monoclonal EIF2S1 (phosphoS51) Abcam Cat#32157; AB_732117 Anti-mouse IgG-HRP Bio-Rad Cat#170-6516; AB_11125142 Anti-mouse 800 nm LiCor IR dye Li-Cor Cat#925-32210; AB_2687825 Anti-rabbit 680 nm LiCor IR dye Li-Cor Cat#926-68076; AB_10956590 Chemicals, Peptides, and Recombinant Proteins Basta, glufosinate ammonium Liberty Cat#280SL SuperSignal TM West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat#34077 SuperSignal TM West Femto Maximum Sensitivity Substrate Thermo Scientific Cat#34085 Hygromycin VWR Cat#80055-268 PMSF Sigma-Aldrich Cat#P7626 Phosphatase Inhibitor Cocktail 2 Millipore Cat#P5726 Luciferin Gold Biotechnology Cat#LUNCA-300 Sodium ortho-vanadate Sigma-Aldrich Cat#S6508 β-glycerophosphate Sigma-Aldrich Cat#G6376 Aprotinin Sigma-Aldrich Cat#A1153 Leupeptin hemisulfate salt Sigma-Aldrich Cat#L2884 Pepstatin A Sigma-Aldrich Cat#P5318 Bathocuproinedisulfonic acid (BCS) Thermo Scientific Cat#164060050 Immobilon-P PVDF membrane Millipore Cat#IPVH00010 Immobilon-FL PVDF membrane Millipore Cat# IPFL00010 Cycloheximide Sigma-Aldrich Cat#C7698-5G Turbo DNase Thermo Fisher Cat#AM2238 RNase I Thermo Fisher Cat#AM2294 CircLigase Epicentre Cat#CL4111K GlycoBlue TM Thermo Fisher Cat#AM9515 miRNeasy Mini Kit Qiagen Cat#217004 T4 RNA ligase 2 truncated New England Biolabs Cat#M0242L SuperScript TM III Reverse Transcriptase Thermo Fisher Cat#18080044 Phusion Hot Start High-Fidelity DNA Polymerase Thermo Fisher Cat#F540L DNA high-sensitivity chip Agilent Cat# 067-4626 Quant-iT TM RiboGreen RNA assay kit Thermo Fisher Cat# R11490 Oligo d(T) 25 Magnetic Beads NEB Cat#S1419S Turbo DNA-free TM Kit Ambion Cat#AM1907 Terminator 5 ′ -Phosphate-Dependent Exonuclease Lucigen Cat#TER51020 SENSE Total RNA-seq Library Preparation Kit Lexogen Cat#009 (Continued on next page) 16 Cell Reports 44, 116484, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER HEPES Sigma Cat#H4034-500G Sodium citrate, dihydrate Millipore Sigma Cat#567446 Paromomycin MP Biochemicals Cat#194535 Dual Glo TM luciferase assay kit Promega Cat#E2920 BCA Protein Assay Kit Thermo Fisher Cat23225 Acetonitrile Fisher Scientific Cat#A9554 Formic Acid Thermo Fisher Cat#28905 Deposited data Circadian intact particle mass spec on ribosomes isolated from WT cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian intact particle mass spec on ribosomes isolated from Δfrq cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian RPF-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282318: GSM8641256 thru GSM8641275 Circadian RNA-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282317: GSM8641276 thru GSM8641295 Raw Data, Mendeley This paper https://doi.org/10.17632/9xpty464cs.1 Experimental models: Organisms/strains Neurospora crassa wild type 74-OR23-IV mat a FGSC FGSC 4200; DBP 985 Neurospora crassa wild type 74-OR23-IV mat A FGSC FGSC 2489; DBP 984 Δmus-51::bar, mat a FGSC FGSC 9718;DBP 641 Δfrq::bar, mat a Bennett et al. 113 DBP 1320 Δfrq::bar, mat A Bennett et al. 113 DBP 1228 Δel-31(ncu08344):hph, mat a This paper DBP 3602 Δel-31(ncu08344):hph, mat A This paper DBP 3274 Complemented Δel-31::hph, Ec el-31 WT , Ec bar + This paper DBP 3585 ras-1 bd , Δel-31::hph, mat A This paper DBP 3280 ras-1 bd , mat A This paper DBP 1582 Δssz-1(ncu00692)::hph FGSC FGSC 14067; DBP 3478 eif-4g::luc translational fusion This paper DBP 4847-4849 Δfrq::bar, eif-4g::luc translational fusion This paper DBP 4850-4853 rrp-15::luc translational fusion This paper DBP 4854-4856 Δfrq::bar, rrp-15::luc translational fusion This paper DBP 4857-4860 ssf-1::luc translational fusion This paper DBP 4775-4776 Δfrq::bar, ssf-1::luc translational fusion This paper DBP 4778, 4779, 4781 gol-9::luc translation fusion This paper DBP 4726 (sib to DBP 4730) or DBP 4735 (sib to DBP4734) Δfrq::bar, gol-9::fluc translation fusion This paper DBP 4730 Δel-31::hph gol-9::fluc translation fusion This paper DBP 4734 tcf-14::luc translation fusion This paper DBP 4302 (sib to DBP 4305) or DBP 4349 (sib to DBP 4354) Δfrq::bar, tcf-14::fluc translation fusion This paper DBP 4305 Δel-31::hph tcf-14::fluc translation fusion This paper DBP 4354 ens-3::fluc translation fusion This paper DBP 4310 (sib to DBP 4312) or DBP 4357 (sib to DBP 4362) (Continued on next page) Cell Reports 44, 116484, November 25, 2025 17 ..

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Hi-C:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    shRNA:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Quantitative RT-PCR:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Fluorescence In Situ Hybridization:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Recombinant:

    Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB Cat#E7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3

    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    Luciferase:

    Article Title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal ScRPL-3 Deposited to the DSHB by Warner, J.R DSHB Hybridoma Product ScRPL3; AB_1553774 Mouse monoclonal anti-HA Roche Cat#11867423001; AB_390918 Mouse monoclonal anti-FRQ Dr. Michael Brunner Clone 3G11-1B10-E2 Rabbit monoclonal EIF2S1 (phosphoS51) Abcam Cat#32157; AB_732117 Anti-mouse IgG-HRP Bio-Rad Cat#170-6516; AB_11125142 Anti-mouse 800 nm LiCor IR dye Li-Cor Cat#925-32210; AB_2687825 Anti-rabbit 680 nm LiCor IR dye Li-Cor Cat#926-68076; AB_10956590 Chemicals, Peptides, and Recombinant Proteins Basta, glufosinate ammonium Liberty Cat#280SL SuperSignal TM West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat#34077 SuperSignal TM West Femto Maximum Sensitivity Substrate Thermo Scientific Cat#34085 Hygromycin VWR Cat#80055-268 PMSF Sigma-Aldrich Cat#P7626 Phosphatase Inhibitor Cocktail 2 Millipore Cat#P5726 Luciferin Gold Biotechnology Cat#LUNCA-300 Sodium ortho-vanadate Sigma-Aldrich Cat#S6508 β-glycerophosphate Sigma-Aldrich Cat#G6376 Aprotinin Sigma-Aldrich Cat#A1153 Leupeptin hemisulfate salt Sigma-Aldrich Cat#L2884 Pepstatin A Sigma-Aldrich Cat#P5318 Bathocuproinedisulfonic acid (BCS) Thermo Scientific Cat#164060050 Immobilon-P PVDF membrane Millipore Cat#IPVH00010 Immobilon-FL PVDF membrane Millipore Cat# IPFL00010 Cycloheximide Sigma-Aldrich Cat#C7698-5G Turbo DNase Thermo Fisher Cat#AM2238 RNase I Thermo Fisher Cat#AM2294 CircLigase Epicentre Cat#CL4111K GlycoBlue TM Thermo Fisher Cat#AM9515 miRNeasy Mini Kit Qiagen Cat#217004 T4 RNA ligase 2 truncated New England Biolabs Cat#M0242L SuperScript TM III Reverse Transcriptase Thermo Fisher Cat#18080044 Phusion Hot Start High-Fidelity DNA Polymerase Thermo Fisher Cat#F540L DNA high-sensitivity chip Agilent Cat# 067-4626 Quant-iT TM RiboGreen RNA assay kit Thermo Fisher Cat# R11490 Oligo d(T) 25 Magnetic Beads NEB Cat#S1419S Turbo DNA-free TM Kit Ambion Cat#AM1907 Terminator 5 ′ -Phosphate-Dependent Exonuclease Lucigen Cat#TER51020 SENSE Total RNA-seq Library Preparation Kit Lexogen Cat#009 (Continued on next page) 16 Cell Reports 44, 116484, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER HEPES Sigma Cat#H4034-500G Sodium citrate, dihydrate Millipore Sigma Cat#567446 Paromomycin MP Biochemicals Cat#194535 Dual Glo TM luciferase assay kit Promega Cat#E2920 BCA Protein Assay Kit Thermo Fisher Cat23225 Acetonitrile Fisher Scientific Cat#A9554 Formic Acid Thermo Fisher Cat#28905 Deposited data Circadian intact particle mass spec on ribosomes isolated from WT cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian intact particle mass spec on ribosomes isolated from Δfrq cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian RPF-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282318: GSM8641256 thru GSM8641275 Circadian RNA-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282317: GSM8641276 thru GSM8641295 Raw Data, Mendeley This paper https://doi.org/10.17632/9xpty464cs.1 Experimental models: Organisms/strains Neurospora crassa wild type 74-OR23-IV mat a FGSC FGSC 4200; DBP 985 Neurospora crassa wild type 74-OR23-IV mat A FGSC FGSC 2489; DBP 984 Δmus-51::bar, mat a FGSC FGSC 9718;DBP 641 Δfrq::bar, mat a Bennett et al. 113 DBP 1320 Δfrq::bar, mat A Bennett et al. 113 DBP 1228 Δel-31(ncu08344):hph, mat a This paper DBP 3602 Δel-31(ncu08344):hph, mat A This paper DBP 3274 Complemented Δel-31::hph, Ec el-31 WT , Ec bar + This paper DBP 3585 ras-1 bd , Δel-31::hph, mat A This paper DBP 3280 ras-1 bd , mat A This paper DBP 1582 Δssz-1(ncu00692)::hph FGSC FGSC 14067; DBP 3478 eif-4g::luc translational fusion This paper DBP 4847-4849 Δfrq::bar, eif-4g::luc translational fusion This paper DBP 4850-4853 rrp-15::luc translational fusion This paper DBP 4854-4856 Δfrq::bar, rrp-15::luc translational fusion This paper DBP 4857-4860 ssf-1::luc translational fusion This paper DBP 4775-4776 Δfrq::bar, ssf-1::luc translational fusion This paper DBP 4778, 4779, 4781 gol-9::luc translation fusion This paper DBP 4726 (sib to DBP 4730) or DBP 4735 (sib to DBP4734) Δfrq::bar, gol-9::fluc translation fusion This paper DBP 4730 Δel-31::hph gol-9::fluc translation fusion This paper DBP 4734 tcf-14::luc translation fusion This paper DBP 4302 (sib to DBP 4305) or DBP 4349 (sib to DBP 4354) Δfrq::bar, tcf-14::fluc translation fusion This paper DBP 4305 Δel-31::hph tcf-14::fluc translation fusion This paper DBP 4354 ens-3::fluc translation fusion This paper DBP 4310 (sib to DBP 4312) or DBP 4357 (sib to DBP 4362) (Continued on next page) Cell Reports 44, 116484, November 25, 2025 17 ..

    Mass Spectrometry:

    Article Title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal ScRPL-3 Deposited to the DSHB by Warner, J.R DSHB Hybridoma Product ScRPL3; AB_1553774 Mouse monoclonal anti-HA Roche Cat#11867423001; AB_390918 Mouse monoclonal anti-FRQ Dr. Michael Brunner Clone 3G11-1B10-E2 Rabbit monoclonal EIF2S1 (phosphoS51) Abcam Cat#32157; AB_732117 Anti-mouse IgG-HRP Bio-Rad Cat#170-6516; AB_11125142 Anti-mouse 800 nm LiCor IR dye Li-Cor Cat#925-32210; AB_2687825 Anti-rabbit 680 nm LiCor IR dye Li-Cor Cat#926-68076; AB_10956590 Chemicals, Peptides, and Recombinant Proteins Basta, glufosinate ammonium Liberty Cat#280SL SuperSignal TM West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat#34077 SuperSignal TM West Femto Maximum Sensitivity Substrate Thermo Scientific Cat#34085 Hygromycin VWR Cat#80055-268 PMSF Sigma-Aldrich Cat#P7626 Phosphatase Inhibitor Cocktail 2 Millipore Cat#P5726 Luciferin Gold Biotechnology Cat#LUNCA-300 Sodium ortho-vanadate Sigma-Aldrich Cat#S6508 β-glycerophosphate Sigma-Aldrich Cat#G6376 Aprotinin Sigma-Aldrich Cat#A1153 Leupeptin hemisulfate salt Sigma-Aldrich Cat#L2884 Pepstatin A Sigma-Aldrich Cat#P5318 Bathocuproinedisulfonic acid (BCS) Thermo Scientific Cat#164060050 Immobilon-P PVDF membrane Millipore Cat#IPVH00010 Immobilon-FL PVDF membrane Millipore Cat# IPFL00010 Cycloheximide Sigma-Aldrich Cat#C7698-5G Turbo DNase Thermo Fisher Cat#AM2238 RNase I Thermo Fisher Cat#AM2294 CircLigase Epicentre Cat#CL4111K GlycoBlue TM Thermo Fisher Cat#AM9515 miRNeasy Mini Kit Qiagen Cat#217004 T4 RNA ligase 2 truncated New England Biolabs Cat#M0242L SuperScript TM III Reverse Transcriptase Thermo Fisher Cat#18080044 Phusion Hot Start High-Fidelity DNA Polymerase Thermo Fisher Cat#F540L DNA high-sensitivity chip Agilent Cat# 067-4626 Quant-iT TM RiboGreen RNA assay kit Thermo Fisher Cat# R11490 Oligo d(T) 25 Magnetic Beads NEB Cat#S1419S Turbo DNA-free TM Kit Ambion Cat#AM1907 Terminator 5 ′ -Phosphate-Dependent Exonuclease Lucigen Cat#TER51020 SENSE Total RNA-seq Library Preparation Kit Lexogen Cat#009 (Continued on next page) 16 Cell Reports 44, 116484, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER HEPES Sigma Cat#H4034-500G Sodium citrate, dihydrate Millipore Sigma Cat#567446 Paromomycin MP Biochemicals Cat#194535 Dual Glo TM luciferase assay kit Promega Cat#E2920 BCA Protein Assay Kit Thermo Fisher Cat23225 Acetonitrile Fisher Scientific Cat#A9554 Formic Acid Thermo Fisher Cat#28905 Deposited data Circadian intact particle mass spec on ribosomes isolated from WT cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian intact particle mass spec on ribosomes isolated from Δfrq cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian RPF-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282318: GSM8641256 thru GSM8641275 Circadian RNA-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282317: GSM8641276 thru GSM8641295 Raw Data, Mendeley This paper https://doi.org/10.17632/9xpty464cs.1 Experimental models: Organisms/strains Neurospora crassa wild type 74-OR23-IV mat a FGSC FGSC 4200; DBP 985 Neurospora crassa wild type 74-OR23-IV mat A FGSC FGSC 2489; DBP 984 Δmus-51::bar, mat a FGSC FGSC 9718;DBP 641 Δfrq::bar, mat a Bennett et al. 113 DBP 1320 Δfrq::bar, mat A Bennett et al. 113 DBP 1228 Δel-31(ncu08344):hph, mat a This paper DBP 3602 Δel-31(ncu08344):hph, mat A This paper DBP 3274 Complemented Δel-31::hph, Ec el-31 WT , Ec bar + This paper DBP 3585 ras-1 bd , Δel-31::hph, mat A This paper DBP 3280 ras-1 bd , mat A This paper DBP 1582 Δssz-1(ncu00692)::hph FGSC FGSC 14067; DBP 3478 eif-4g::luc translational fusion This paper DBP 4847-4849 Δfrq::bar, eif-4g::luc translational fusion This paper DBP 4850-4853 rrp-15::luc translational fusion This paper DBP 4854-4856 Δfrq::bar, rrp-15::luc translational fusion This paper DBP 4857-4860 ssf-1::luc translational fusion This paper DBP 4775-4776 Δfrq::bar, ssf-1::luc translational fusion This paper DBP 4778, 4779, 4781 gol-9::luc translation fusion This paper DBP 4726 (sib to DBP 4730) or DBP 4735 (sib to DBP4734) Δfrq::bar, gol-9::fluc translation fusion This paper DBP 4730 Δel-31::hph gol-9::fluc translation fusion This paper DBP 4734 tcf-14::luc translation fusion This paper DBP 4302 (sib to DBP 4305) or DBP 4349 (sib to DBP 4354) Δfrq::bar, tcf-14::fluc translation fusion This paper DBP 4305 Δel-31::hph tcf-14::fluc translation fusion This paper DBP 4354 ens-3::fluc translation fusion This paper DBP 4310 (sib to DBP 4312) or DBP 4357 (sib to DBP 4362) (Continued on next page) Cell Reports 44, 116484, November 25, 2025 17 ..

    Isolation:

    Article Title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal ScRPL-3 Deposited to the DSHB by Warner, J.R DSHB Hybridoma Product ScRPL3; AB_1553774 Mouse monoclonal anti-HA Roche Cat#11867423001; AB_390918 Mouse monoclonal anti-FRQ Dr. Michael Brunner Clone 3G11-1B10-E2 Rabbit monoclonal EIF2S1 (phosphoS51) Abcam Cat#32157; AB_732117 Anti-mouse IgG-HRP Bio-Rad Cat#170-6516; AB_11125142 Anti-mouse 800 nm LiCor IR dye Li-Cor Cat#925-32210; AB_2687825 Anti-rabbit 680 nm LiCor IR dye Li-Cor Cat#926-68076; AB_10956590 Chemicals, Peptides, and Recombinant Proteins Basta, glufosinate ammonium Liberty Cat#280SL SuperSignal TM West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat#34077 SuperSignal TM West Femto Maximum Sensitivity Substrate Thermo Scientific Cat#34085 Hygromycin VWR Cat#80055-268 PMSF Sigma-Aldrich Cat#P7626 Phosphatase Inhibitor Cocktail 2 Millipore Cat#P5726 Luciferin Gold Biotechnology Cat#LUNCA-300 Sodium ortho-vanadate Sigma-Aldrich Cat#S6508 β-glycerophosphate Sigma-Aldrich Cat#G6376 Aprotinin Sigma-Aldrich Cat#A1153 Leupeptin hemisulfate salt Sigma-Aldrich Cat#L2884 Pepstatin A Sigma-Aldrich Cat#P5318 Bathocuproinedisulfonic acid (BCS) Thermo Scientific Cat#164060050 Immobilon-P PVDF membrane Millipore Cat#IPVH00010 Immobilon-FL PVDF membrane Millipore Cat# IPFL00010 Cycloheximide Sigma-Aldrich Cat#C7698-5G Turbo DNase Thermo Fisher Cat#AM2238 RNase I Thermo Fisher Cat#AM2294 CircLigase Epicentre Cat#CL4111K GlycoBlue TM Thermo Fisher Cat#AM9515 miRNeasy Mini Kit Qiagen Cat#217004 T4 RNA ligase 2 truncated New England Biolabs Cat#M0242L SuperScript TM III Reverse Transcriptase Thermo Fisher Cat#18080044 Phusion Hot Start High-Fidelity DNA Polymerase Thermo Fisher Cat#F540L DNA high-sensitivity chip Agilent Cat# 067-4626 Quant-iT TM RiboGreen RNA assay kit Thermo Fisher Cat# R11490 Oligo d(T) 25 Magnetic Beads NEB Cat#S1419S Turbo DNA-free TM Kit Ambion Cat#AM1907 Terminator 5 ′ -Phosphate-Dependent Exonuclease Lucigen Cat#TER51020 SENSE Total RNA-seq Library Preparation Kit Lexogen Cat#009 (Continued on next page) 16 Cell Reports 44, 116484, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER HEPES Sigma Cat#H4034-500G Sodium citrate, dihydrate Millipore Sigma Cat#567446 Paromomycin MP Biochemicals Cat#194535 Dual Glo TM luciferase assay kit Promega Cat#E2920 BCA Protein Assay Kit Thermo Fisher Cat23225 Acetonitrile Fisher Scientific Cat#A9554 Formic Acid Thermo Fisher Cat#28905 Deposited data Circadian intact particle mass spec on ribosomes isolated from WT cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian intact particle mass spec on ribosomes isolated from Δfrq cells, DD12-DD48 This paper massive.ucsd.edu: user: MSV000096101 password: Clock6057 Circadian RPF-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282318: GSM8641256 thru GSM8641275 Circadian RNA-seq DD12-DD48 of Δel31 cells This paper GEO: GSE282317: GSM8641276 thru GSM8641295 Raw Data, Mendeley This paper https://doi.org/10.17632/9xpty464cs.1 Experimental models: Organisms/strains Neurospora crassa wild type 74-OR23-IV mat a FGSC FGSC 4200; DBP 985 Neurospora crassa wild type 74-OR23-IV mat A FGSC FGSC 2489; DBP 984 Δmus-51::bar, mat a FGSC FGSC 9718;DBP 641 Δfrq::bar, mat a Bennett et al. 113 DBP 1320 Δfrq::bar, mat A Bennett et al. 113 DBP 1228 Δel-31(ncu08344):hph, mat a This paper DBP 3602 Δel-31(ncu08344):hph, mat A This paper DBP 3274 Complemented Δel-31::hph, Ec el-31 WT , Ec bar + This paper DBP 3585 ras-1 bd , Δel-31::hph, mat A This paper DBP 3280 ras-1 bd , mat A This paper DBP 1582 Δssz-1(ncu00692)::hph FGSC FGSC 14067; DBP 3478 eif-4g::luc translational fusion This paper DBP 4847-4849 Δfrq::bar, eif-4g::luc translational fusion This paper DBP 4850-4853 rrp-15::luc translational fusion This paper DBP 4854-4856 Δfrq::bar, rrp-15::luc translational fusion This paper DBP 4857-4860 ssf-1::luc translational fusion This paper DBP 4775-4776 Δfrq::bar, ssf-1::luc translational fusion This paper DBP 4778, 4779, 4781 gol-9::luc translation fusion This paper DBP 4726 (sib to DBP 4730) or DBP 4735 (sib to DBP4734) Δfrq::bar, gol-9::fluc translation fusion This paper DBP 4730 Δel-31::hph gol-9::fluc translation fusion This paper DBP 4734 tcf-14::luc translation fusion This paper DBP 4302 (sib to DBP 4305) or DBP 4349 (sib to DBP 4354) Δfrq::bar, tcf-14::fluc translation fusion This paper DBP 4305 Δel-31::hph tcf-14::fluc translation fusion This paper DBP 4354 ens-3::fluc translation fusion This paper DBP 4310 (sib to DBP 4312) or DBP 4357 (sib to DBP 4362) (Continued on next page) Cell Reports 44, 116484, November 25, 2025 17 ..

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    SYBR Green Assay:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Plasmid Preparation:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    LDH Cytotoxicity Assay:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Purification:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    AST Assay:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Activity Assay:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Glucose Assay:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Software:

    Article Title: Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DTT MCE Cat# HY-15917 Laurdan, MCE Cat# HY-D0080 Ceapin-A7 MCE Cat# HY-108434 C29 MCE Cat# HY-100461 Larminaran MCE Cat# HY-119109 Atorvastatin MCE Cat# HY-B0589 Myriocin MCE Cat# HY-N6798 IPTG MCE Cat# HY-15921 Critical commercial assays Zombie Violet Fixable Viability kit Biolegend Cat# 423114 PrimeScript RT-PCR Kit Takara Cat# RR037A SYBR Green PCR Master Mix Roche Cat# 04887352001 Plasmid DNA Midi Kit OMEGA Cat# D6904-01 RNA fast200 Kit Fastagen Cat# 220011 Reactive Oxygen Species Assay Kit (DHE) Applygen Cat# C1300-2 10X Kinase buffer Cell Signaling Technology Cat# 9802 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23227 Super Signal West Pico PLUS Thermo Fisher Cat# 34578 Super Signal West Dura Thermo Fisher Cat# 34075 LDH Cytotoxicity Assay Kit Beyotime Cat# C0016 PBMC Isolation Kit Beyotime Cat# P8680 GST tag purification kit Beyotime Cat# P2262 Amplex Red Aspartate Aminotransferase Activity Assay Kit Beyotime Cat#P2715 Amplex Red Alanine Aminotransferase Activity Assay Kit Beyotime Cat#P2711 Glucose Assay Kit with O-toluidine Beyotime Cat#S0201 Oligonucleotides qRT-PCR primers Table S1 N/A Software and algorithms CytExpert Beckman Coulter https://www.beckman.com Imaris Oxford Instruments https://imaris.oxinst.com GraphPad Prism8 Graphpad https://www.graphpad.com ImageJ N/A https://imagej.net/software/fiji 20 Cell Reports 45, 116976, February 24, 2026 Assessment and Accreditation of Laboratory Animal Care, and performed with approval from Scientific Investigation Board of the Medical School of Shandong University. ..

    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Sequencing:

    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Cell Culture:

    Article Title: Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
    Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Psychrobacter sp. D2 Zhang Laboratory NCBI: JACDXZ000000000 ΔdddT This study ΔdddT/pBBRMCS2-dddT This study E. coli WM3064 Dehio and Meyer, 1997 E. coli DH5α Vazyme Biotech Company, China Cat # C502-02 E. coli C43 (DE3) WEIDI Biotechnology Company, China Cat # EC1040 Recombinant DNA pK18mobsacB-Ery Wang et al, 2015b pK18mobsacB-Ery- dddT This study pET-22b-dddT This study pET-22b-Bba-dddT This study pBBR1MCS2 Kovach et al, 1995 pBBR1MCS2-dddT This study 10 The EMBO Journal © The Author(s) Reagent/resource Reference or source Identifier or catalog number Antibodies Anti-His Tag Monoclonal antibody Solarbio, China Cat # K200060M Anti-GAPDH rabbit polyclonal antibody Sangon Biotech, China Cat # D110016 HRP-labeled Goat Antimouse IgG(H+ L) Beyotime, China Cat # A0350 HRP-labeled Goat AntiRabbit IgG(H+ L) Beyotime, China Cat # A0352 Oligonucleotides and other sequence-based reagents PCR primers This study Appendix Table S3 Chemicals, enzymes, and other reagents FastPfu DNA Polymerase TransGenBiotech, China Cat # AP221-01 In-Fusion Snap Assembly Maser Mix TaKaRa, Japan Cat # 638947 Pierce BCA Protein Assay Kit Thermo Fisher, USA Cat # 23227 Software cryoSPARC Punjani et al, 2017 UCSF Chimera Pettersen et al, 2004 COOT Casañal et al, 2020 Phenix Liebschner et al, 2019 MolProbity 4 Williams et al, 2018 ChimeraX Pettersen et al, 2021 Other Bacterial strains and growth conditions P. sp. D2 and its mutants and supplemental strains were cultured in marine broth 2216E medium or the basal medium (Appendix Table S4) supplemented with 6 mM DMSP, glucose, or succinate as the carbon source at 20 °C. ..

    Control:

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    Virus:

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    Protease Inhibitor:

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    Mutagenesis:

    Article Title: Pharmacologic interrogation of USP28 cellular function in p53 signaling.
    Article Snippet: Article Pharmacologic interrogation of USP28 cellular function in p53 signaling

    DNA Extraction:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Enzyme-linked Immunosorbent Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    ROS Assay:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..

    Microarray:

    Article Title: Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Discovery OmniMap anti-Rabbit HRP conjugate Roche Cat #760-4311; RRID: AB_2811043 Bond Polymer Refine Detection kit Leica Cat # DS9800; RRID: AB_2891238 Bacterial and virus strains Streptococcus pneumoniae: serotype 4 strain: TIGR4 Rosch Laboratory strain N/A Mouse-adapted A/California/04/2009 H1N1 Influenza Virus Schultz-Cherry Laboratory strain N/A Biological samples Sorted cells from ASD+/- and ASD+/+ tumor stroma for microarray analysis This paper N/A Mononuclear cells from ASD+/- and ASD+/+ tumor and tumor stroma for single cell RNA-seq This paper N/A Human DICER1+/+ and DICER1+/- FN-RMS Samples This paper; International Pleuropulmonary Blastoma/DICER1 Registry N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium, DMEM high glucose HyClone Cat #SH30243.01 USDA Import Tested Fetal Bovine Serum (FBS) HyClone Cat #SH30910.03 Antibiotic/ antimycotic Sigma-Aldrich Cat #A5955 Roswell Park Memorial Institute (RPMI) 1640 Medium Gibco Cat #11835055 Neurobasal Media Invitrogen Cat #21103049 EGF R&D Systems Cat #236-EG b-FGF R&D Systems Cat #3718-FB B27 Gibco Cat #17504044 GlutaMAX Gibco Cat # 35050-061 QIAzol lysis reagent Qiagen Cat #79306 Collagenase B Roche Cat #11088831001 Dispase II Roche Cat #04942078001 Accumax Solution Sigma-Aldrich Cat #2026-02-28 Matrigel Matrix Corning Cat #354234 Live/Dead Blue Thermo Fisher Cat #L34962 Bovine serum albumin (BSA) Sigma-Aldrich Cat #A7159 Histoclear National Diagnostics Cat # HS-200 Fc Receptor Blocker Innovex Cat #NB309 FuGENE6 Promega Cat #E2691 LL-37 Tocris Cat #5213 Erlotinib MedChemExpress Cat #HY-50896 Linsitinib MedChemExpress Cat #HY-10191 GSK199 Cayman Chemical Cat #17489 cOmpleteTM Protease Inhibitor Cocktail Roche Cat #11697498001 PhosSTOP Roche Cat #4906845001 Triton X-100 Sigma-Aldrich Cat #T8787 ACK Lysing Buffer Gibco Cat #A1049201 Complement Component C5a Biotechne Cat #2150-C5-025/CF ProLong Diamond Antifade Mountant Invitrogen Cat #P36961 Ficoll-Paque Plus GE Healthcare 17-1440-02 Phorbol 12-myristate 13 acetate (PMA) Tocris Cat #1201 A23187 Cayman Chemical Cat #11016 (Continued on next page) ll OPEN ACCESSArticle Developmental Cell 61, 1–17.e1–e12, January 14, 2026 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER pHrodo E. coli BioParticles conjugate for phagocytosis Invitrogen Cat #P35361 Disulfiram (Tetraethylthiuram disulfide) Sigma Aldrich Cat #86720-50G Critical commercial assays miRNeasy Micro Kit Qiagen Cat #217084 miRNeasy mini Kit Qiagen Cat #217004 Superscript III First Strand cDNA Synthesis Kit Thermo Fisher Cat #18080051 Fast SYBR Green Master Mix Thermo Fisher Cat #4385610 TaqMan Fast Advanced Master Mix Thermo Fisher Cat #4444964 PicoPure DNA Extraction Kit Thermo Fisher Cat #KIT0103 DNeasy Blood and Tissue Kit Qiagen Cat #69504 Pierce BCA Protein Assay Kit Thermo Fisher Cat #23225 Proteome Profilers Mouse Cytokine Array Kit, Panel A R&D Systems Cat #ARY006 Mouse Complement C5a ELISA Kit Abcam Cat #ab193718 KAPA RNA HyperPrep Kit with RiboErase Roche Cat #08098131702 DCFDA/H2DFDA Cellular ROS Assay Kit Abcam Cat #ab113851 Neutrophil Myeloperoxidase Activity Assay Kit Cayman Chemical Cat #600620 Neutrophil Elastase Activity Assay Kit Cayman Chemical Cat #600610 Deposited data Microarray data – purified murine ASD+/- FN-RMS tumor stroma This paper GSE264568 Microarray data – purified murine ASD+/+ FN-RMS tumor stroma Drummond et al.12 GSE98059 scRNA-seq – purified murine ASD+/+ and ASD+/- FN- RMS tumor and stroma This paper GSE264567 Bulk RNA-seq – human DICER1+/+ and DICER1+/- FN-RMS tumors This paper GSE264566 Human FN-RMS bulk RNA-seq from the St. Jude Pediatric Cancer Genome Project and Genomes 4 Kids Project https://pecan.stjude.cloud/ N/A T cell exhaustion gene sets Wherry et al.58 GSE9650 Experimental models: Cell lines ..



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