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    Structured Review

    Zymo Research sequencing
    Sequencing, supplied by Zymo Research, used in various techniques. Bioz Stars score: 93/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip-seq/ChIP-Seq/pm34021049-180-2-27
    Average 93 stars, based on 43 article reviews
    sequencing - by Bioz Stars, 2026-09
    93/100 stars

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    Related Articles

    Chromatin Immunoprecipitation:

    Article Title: Integrated multi-omic analysis reveals KDM5B as a regulator of microglial reactivity to immunomodulatory stimuli
    Article Snippet: .. Full ChIP-seq service was performed by Zymo Research Corporation (Irvine, CA). .. Chromatin was extracted from formaldehyde cross-linked mouse primary microglia using the Zymo-Spin TM ChIP kit (Zymo Research Corp., Irvine, CA).

    Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease.
    Article Snippet: Chromatin was collected by centrifugation (14,000xg, 10 min at 4C) and quantified (Qubit 4 Fluorometer, Agilent TapeStation). .. Native H3K4me3 ChIP-seq was REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Senseera cfChIP-seq kit https://www.senseerahealth.com/ Zymo cfDNA extraction kit Zymo Research ZR-R1072 Chemicals, peptides, and recombinant proteins protease inhibitors Roche 5056489001 Micrococcal nuclease Worthington Biochemical LS004798 Bovine Serum Heat inactivated Rockland D500-05-0500 Software and algorithms cfChIP-seq analysis Sadeh et al.42 https://github.com/nirfriedman/cfChIP-seq; https://doi.org/ 10.5281/zenodo.15766044 cfChIP-seq urine specific setup files This study https://doi.org/10.5281/zenodo.3967253 bowtie2 (2.4.2) Langmead et al., 201289 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml samtools (1.7) Li et al., 200990 https://www.htslib.org/ R programming language (4.0.2) https://www.r-project.org/ Deposited data cfChiP-seq data This study https://doi.org/10.5281/zenodo.15227938 Raw and analyzed ChIP-seq ENCODE3 project https://www.encodeproject.org/ Raw and analyzed ChIP-seq BLUEPRINT project https://epigenomesportal.ca/ihec/ Cell Genomics 5, 100974, October 8, 2025 e1 performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq. .. cfDNA from urine samples (collected as above) was extracted using Zymo cfDNA extraction kit [Zymo Research ZR-R1072] according to manufacturer’s instructions.

    Article Title: Clr4 SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation.
    Article Snippet: .. Total ChIP-seq read counts for defined region were analyzed using MultiBigwigSummary or MultiBamSummary. sRNA-seq For sRNA-seq, total RNAs were purified from freshly grown yeast cells using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymoresearch R2014) and sRNA were enriched using RNA Clean & Concentrator (Zymoresearch R1013). sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina (NEB E7330) and barcodedmultiplex libraries were sequenced using Illumina MiSeq platform, which generates single-end 36 nt reads. ..

    Extraction:

    Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease.
    Article Snippet: Chromatin was collected by centrifugation (14,000xg, 10 min at 4C) and quantified (Qubit 4 Fluorometer, Agilent TapeStation). .. Native H3K4me3 ChIP-seq was REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Senseera cfChIP-seq kit https://www.senseerahealth.com/ Zymo cfDNA extraction kit Zymo Research ZR-R1072 Chemicals, peptides, and recombinant proteins protease inhibitors Roche 5056489001 Micrococcal nuclease Worthington Biochemical LS004798 Bovine Serum Heat inactivated Rockland D500-05-0500 Software and algorithms cfChIP-seq analysis Sadeh et al.42 https://github.com/nirfriedman/cfChIP-seq; https://doi.org/ 10.5281/zenodo.15766044 cfChIP-seq urine specific setup files This study https://doi.org/10.5281/zenodo.3967253 bowtie2 (2.4.2) Langmead et al., 201289 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml samtools (1.7) Li et al., 200990 https://www.htslib.org/ R programming language (4.0.2) https://www.r-project.org/ Deposited data cfChiP-seq data This study https://doi.org/10.5281/zenodo.15227938 Raw and analyzed ChIP-seq ENCODE3 project https://www.encodeproject.org/ Raw and analyzed ChIP-seq BLUEPRINT project https://epigenomesportal.ca/ihec/ Cell Genomics 5, 100974, October 8, 2025 e1 performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq. .. cfDNA from urine samples (collected as above) was extracted using Zymo cfDNA extraction kit [Zymo Research ZR-R1072] according to manufacturer’s instructions.

    Recombinant:

    Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease.
    Article Snippet: Chromatin was collected by centrifugation (14,000xg, 10 min at 4C) and quantified (Qubit 4 Fluorometer, Agilent TapeStation). .. Native H3K4me3 ChIP-seq was REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Senseera cfChIP-seq kit https://www.senseerahealth.com/ Zymo cfDNA extraction kit Zymo Research ZR-R1072 Chemicals, peptides, and recombinant proteins protease inhibitors Roche 5056489001 Micrococcal nuclease Worthington Biochemical LS004798 Bovine Serum Heat inactivated Rockland D500-05-0500 Software and algorithms cfChIP-seq analysis Sadeh et al.42 https://github.com/nirfriedman/cfChIP-seq; https://doi.org/ 10.5281/zenodo.15766044 cfChIP-seq urine specific setup files This study https://doi.org/10.5281/zenodo.3967253 bowtie2 (2.4.2) Langmead et al., 201289 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml samtools (1.7) Li et al., 200990 https://www.htslib.org/ R programming language (4.0.2) https://www.r-project.org/ Deposited data cfChiP-seq data This study https://doi.org/10.5281/zenodo.15227938 Raw and analyzed ChIP-seq ENCODE3 project https://www.encodeproject.org/ Raw and analyzed ChIP-seq BLUEPRINT project https://epigenomesportal.ca/ihec/ Cell Genomics 5, 100974, October 8, 2025 e1 performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq. .. cfDNA from urine samples (collected as above) was extracted using Zymo cfDNA extraction kit [Zymo Research ZR-R1072] according to manufacturer’s instructions.

    Software:

    Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease.
    Article Snippet: Chromatin was collected by centrifugation (14,000xg, 10 min at 4C) and quantified (Qubit 4 Fluorometer, Agilent TapeStation). .. Native H3K4me3 ChIP-seq was REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Senseera cfChIP-seq kit https://www.senseerahealth.com/ Zymo cfDNA extraction kit Zymo Research ZR-R1072 Chemicals, peptides, and recombinant proteins protease inhibitors Roche 5056489001 Micrococcal nuclease Worthington Biochemical LS004798 Bovine Serum Heat inactivated Rockland D500-05-0500 Software and algorithms cfChIP-seq analysis Sadeh et al.42 https://github.com/nirfriedman/cfChIP-seq; https://doi.org/ 10.5281/zenodo.15766044 cfChIP-seq urine specific setup files This study https://doi.org/10.5281/zenodo.3967253 bowtie2 (2.4.2) Langmead et al., 201289 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml samtools (1.7) Li et al., 200990 https://www.htslib.org/ R programming language (4.0.2) https://www.r-project.org/ Deposited data cfChiP-seq data This study https://doi.org/10.5281/zenodo.15227938 Raw and analyzed ChIP-seq ENCODE3 project https://www.encodeproject.org/ Raw and analyzed ChIP-seq BLUEPRINT project https://epigenomesportal.ca/ihec/ Cell Genomics 5, 100974, October 8, 2025 e1 performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq. .. cfDNA from urine samples (collected as above) was extracted using Zymo cfDNA extraction kit [Zymo Research ZR-R1072] according to manufacturer’s instructions.

    other:

    Article Title: Promoter strength and position govern promoter competition
    Article Snippet: For ChIP-seq, DNA was extracted with phenol chloroform extraction and for ChIP-qPCR samples were processed using Zymo Clean& Concentrator-5 kit.

    Article Title: Reciprocal inhibition of NOTCH and SOX2 shapes tumor cell plasticity and therapeutic escape in triple-negative breast cancer.
    Article Snippet: Cancer cell plasticity contributes significantly to the failure of chemoand targeted therapies in triple-negative breast cancer (TNBC).. Molecular mechanisms of therapy-induced tumor cell plasticity and associated resistance are largely unknown.. Using a genome-wide CRISPR-Cas9 screen, we investigated escape mechanisms of NOTCH-driven TNBC treated with a gammasecretase inhibitor (GSI) and identified SOX2 as a target of resistance to Notch inhibition.

    Article Title: Dual action of macrophage miR-204 confines cyclosporine A-induced atherosclerosis.
    Article Snippet: Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China Department of Pharmacy, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China Department of Pharmacology, College of Pharmacy, Harbin Medical University, Heilongjiang Academy of Medical Sciences, Harbin, China Program of Kidney and Cardiovascular Diseases, the Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China Division of Cardiac Surgery, The Key Laboratory of Assisted Circulation, Ministry of Health, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China

    Real-time Polymerase Chain Reaction:


    RNA Extraction:


    Protease Inhibitor:

    Article Title: Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mineral oil Cooper Surgical ART-4008-P G-MOPS Plus buffer Vitrolife 10173 DNAse I Roche 03724778103 DAPI Sigma D8417-1MG Vectashield Vector Laboratories H-1000 Polybrene Millipore TR-1003-G DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12), GlutaMAX supplement Thermo Fisher Scientific 31331093 Advanced DMEM/F-12 Thermo Fisher Scientific 12634010 2-Mercaptoethanol Thermo Fisher Scientific 31350 BSA solution Sigma-Aldrich A8412 Insulin-Transferrin-Selenium-Ethanolamine (ITS -X) supplement Thermo Fisher Scientific 51500056 Forskolin Sigma-Aldrich 93049 Knockout serum replacement (KSR) Thermo Fisher Scientific 10828010 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Corning 356231 N2 supplement Thermo Fisher Scientific 17502048 B27 supplement minus vitamin A Thermo Fisher Scientific 12587010 Primocin InvivoGen ant-pm-1 N-acetyl-L cysteine Sigma-Aldrich A9165 L-glutamine Sigma-Aldrich 25030024 recombinant human EGF Peprotech AF10015 CHIR99021 Tocris 4423 recombinant human R-spondin-1 R&D systems 4645-RS-01M/CF recombinant human FGF-2 Peprotech 100-18B recombinant human HGF Peprotech 100-39 A83-01 Tocris 2939 prostaglandin E2 Sigma-Aldrich P0409 Y27632 Millipore 688000 Enzima TrypLE Express Thermo Fisher Scientific 12604013 Cultrex mouse collagen IV R&D Systems 3410-010-02 Human NRG1-beta1 Cell Signaling 26941S Cell Recovery Solution Corning 354253 IGEPAL CA-630 Sigma-Aldrich 56741 Precision Plus Protein Dual Colour Standards BioRad 1610374 PVDF blotting membranes Millipore IPVH00010 enhanced chemiluminescence reaction GE Healthcare RPN2209 poly-vinylpyrrolidone Sigma P0930 Fetal Bovine Serum Thermo Fisher Scientific 10270106 Proteinase K Thermo Fisher Scientific EO0491 20% SDS solution Sigma 161-0418 Exonuclease I New England Biolabs M0293S Klenow Fragment (3’->5’ exo-) New England Biolabs M0212S Phusion High-Fidelity DNA polymerase Thermo Scientific F-530S TRIzol Invitrogen 15596026 Chloroform:isoamyl alcohol Sigma 25666 GlycoBlue Thermo Fisher Scientific AM9515 (Continued on next page) Cell Stem Cell 32, 1–17.e1–e9, February 6, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F

    RNA Sequencing:

    Article Title: Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mineral oil Cooper Surgical ART-4008-P G-MOPS Plus buffer Vitrolife 10173 DNAse I Roche 03724778103 DAPI Sigma D8417-1MG Vectashield Vector Laboratories H-1000 Polybrene Millipore TR-1003-G DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12), GlutaMAX supplement Thermo Fisher Scientific 31331093 Advanced DMEM/F-12 Thermo Fisher Scientific 12634010 2-Mercaptoethanol Thermo Fisher Scientific 31350 BSA solution Sigma-Aldrich A8412 Insulin-Transferrin-Selenium-Ethanolamine (ITS -X) supplement Thermo Fisher Scientific 51500056 Forskolin Sigma-Aldrich 93049 Knockout serum replacement (KSR) Thermo Fisher Scientific 10828010 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Corning 356231 N2 supplement Thermo Fisher Scientific 17502048 B27 supplement minus vitamin A Thermo Fisher Scientific 12587010 Primocin InvivoGen ant-pm-1 N-acetyl-L cysteine Sigma-Aldrich A9165 L-glutamine Sigma-Aldrich 25030024 recombinant human EGF Peprotech AF10015 CHIR99021 Tocris 4423 recombinant human R-spondin-1 R&D systems 4645-RS-01M/CF recombinant human FGF-2 Peprotech 100-18B recombinant human HGF Peprotech 100-39 A83-01 Tocris 2939 prostaglandin E2 Sigma-Aldrich P0409 Y27632 Millipore 688000 Enzima TrypLE Express Thermo Fisher Scientific 12604013 Cultrex mouse collagen IV R&D Systems 3410-010-02 Human NRG1-beta1 Cell Signaling 26941S Cell Recovery Solution Corning 354253 IGEPAL CA-630 Sigma-Aldrich 56741 Precision Plus Protein Dual Colour Standards BioRad 1610374 PVDF blotting membranes Millipore IPVH00010 enhanced chemiluminescence reaction GE Healthcare RPN2209 poly-vinylpyrrolidone Sigma P0930 Fetal Bovine Serum Thermo Fisher Scientific 10270106 Proteinase K Thermo Fisher Scientific EO0491 20% SDS solution Sigma 161-0418 Exonuclease I New England Biolabs M0293S Klenow Fragment (3’->5’ exo-) New England Biolabs M0212S Phusion High-Fidelity DNA polymerase Thermo Scientific F-530S TRIzol Invitrogen 15596026 Chloroform:isoamyl alcohol Sigma 25666 GlycoBlue Thermo Fisher Scientific AM9515 (Continued on next page) Cell Stem Cell 32, 1–17.e1–e9, February 6, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F

    DNA Methylation Assay:

    Article Title: Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mineral oil Cooper Surgical ART-4008-P G-MOPS Plus buffer Vitrolife 10173 DNAse I Roche 03724778103 DAPI Sigma D8417-1MG Vectashield Vector Laboratories H-1000 Polybrene Millipore TR-1003-G DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12), GlutaMAX supplement Thermo Fisher Scientific 31331093 Advanced DMEM/F-12 Thermo Fisher Scientific 12634010 2-Mercaptoethanol Thermo Fisher Scientific 31350 BSA solution Sigma-Aldrich A8412 Insulin-Transferrin-Selenium-Ethanolamine (ITS -X) supplement Thermo Fisher Scientific 51500056 Forskolin Sigma-Aldrich 93049 Knockout serum replacement (KSR) Thermo Fisher Scientific 10828010 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Corning 356231 N2 supplement Thermo Fisher Scientific 17502048 B27 supplement minus vitamin A Thermo Fisher Scientific 12587010 Primocin InvivoGen ant-pm-1 N-acetyl-L cysteine Sigma-Aldrich A9165 L-glutamine Sigma-Aldrich 25030024 recombinant human EGF Peprotech AF10015 CHIR99021 Tocris 4423 recombinant human R-spondin-1 R&D systems 4645-RS-01M/CF recombinant human FGF-2 Peprotech 100-18B recombinant human HGF Peprotech 100-39 A83-01 Tocris 2939 prostaglandin E2 Sigma-Aldrich P0409 Y27632 Millipore 688000 Enzima TrypLE Express Thermo Fisher Scientific 12604013 Cultrex mouse collagen IV R&D Systems 3410-010-02 Human NRG1-beta1 Cell Signaling 26941S Cell Recovery Solution Corning 354253 IGEPAL CA-630 Sigma-Aldrich 56741 Precision Plus Protein Dual Colour Standards BioRad 1610374 PVDF blotting membranes Millipore IPVH00010 enhanced chemiluminescence reaction GE Healthcare RPN2209 poly-vinylpyrrolidone Sigma P0930 Fetal Bovine Serum Thermo Fisher Scientific 10270106 Proteinase K Thermo Fisher Scientific EO0491 20% SDS solution Sigma 161-0418 Exonuclease I New England Biolabs M0293S Klenow Fragment (3’->5’ exo-) New England Biolabs M0212S Phusion High-Fidelity DNA polymerase Thermo Scientific F-530S TRIzol Invitrogen 15596026 Chloroform:isoamyl alcohol Sigma 25666 GlycoBlue Thermo Fisher Scientific AM9515 (Continued on next page) Cell Stem Cell 32, 1–17.e1–e9, February 6, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F

    Isolation:

    Article Title: Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mineral oil Cooper Surgical ART-4008-P G-MOPS Plus buffer Vitrolife 10173 DNAse I Roche 03724778103 DAPI Sigma D8417-1MG Vectashield Vector Laboratories H-1000 Polybrene Millipore TR-1003-G DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12), GlutaMAX supplement Thermo Fisher Scientific 31331093 Advanced DMEM/F-12 Thermo Fisher Scientific 12634010 2-Mercaptoethanol Thermo Fisher Scientific 31350 BSA solution Sigma-Aldrich A8412 Insulin-Transferrin-Selenium-Ethanolamine (ITS -X) supplement Thermo Fisher Scientific 51500056 Forskolin Sigma-Aldrich 93049 Knockout serum replacement (KSR) Thermo Fisher Scientific 10828010 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Corning 356231 N2 supplement Thermo Fisher Scientific 17502048 B27 supplement minus vitamin A Thermo Fisher Scientific 12587010 Primocin InvivoGen ant-pm-1 N-acetyl-L cysteine Sigma-Aldrich A9165 L-glutamine Sigma-Aldrich 25030024 recombinant human EGF Peprotech AF10015 CHIR99021 Tocris 4423 recombinant human R-spondin-1 R&D systems 4645-RS-01M/CF recombinant human FGF-2 Peprotech 100-18B recombinant human HGF Peprotech 100-39 A83-01 Tocris 2939 prostaglandin E2 Sigma-Aldrich P0409 Y27632 Millipore 688000 Enzima TrypLE Express Thermo Fisher Scientific 12604013 Cultrex mouse collagen IV R&D Systems 3410-010-02 Human NRG1-beta1 Cell Signaling 26941S Cell Recovery Solution Corning 354253 IGEPAL CA-630 Sigma-Aldrich 56741 Precision Plus Protein Dual Colour Standards BioRad 1610374 PVDF blotting membranes Millipore IPVH00010 enhanced chemiluminescence reaction GE Healthcare RPN2209 poly-vinylpyrrolidone Sigma P0930 Fetal Bovine Serum Thermo Fisher Scientific 10270106 Proteinase K Thermo Fisher Scientific EO0491 20% SDS solution Sigma 161-0418 Exonuclease I New England Biolabs M0293S Klenow Fragment (3’->5’ exo-) New England Biolabs M0212S Phusion High-Fidelity DNA polymerase Thermo Scientific F-530S TRIzol Invitrogen 15596026 Chloroform:isoamyl alcohol Sigma 25666 GlycoBlue Thermo Fisher Scientific AM9515 (Continued on next page) Cell Stem Cell 32, 1–17.e1–e9, February 6, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F .. REAGENT or RESOURCE SOURCE IDENTIFIER GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Sigma GE65152105050250 Dynabeads M-280 Streptavidin Thermo Fisher Scientific 11205D AMPure XP Bead-Based Reagent Beckman Coulter A63880 Micrococcal nuclease New England Biolabs M0247S Buffer EB Qiagen 19086 Dynabeads Protein A Thermo Fisher Scientific 10002D Dynabeads Protein G Thermo Fisher Scientific 10004D PMSF Sigma P7626 Protease inhibitor cocktail Sigma P8340 Triton X-100 Sigma X100 Sodium Deoxycholate Merck D6750-10G Critical commercial assays LIVE/DEAD Fixable Zombie Aqua Thermo Fisher Scientific L10119 MicroPlex Library Preparation kit Diagenode C05010001 Dynabeads mRNA DIRECT kit Thermo Fisher Scientific 61011 SMARTer Stranded RNA-seq kit Takara 634836 KAPA Library Quanitification Kit Roche KK4824 Bioanalyzer High DNA Sensitivity chip kit Agilent 5067-4626 RNeasy Mini Kit Qiagen 74104 PrimeScript RT Master Mix Takara Bio RR036B TB Green Premix Ex Taq Takara Bio RR820L EZ DNA Methylation Direct Kit Zymo Research D5020 Nuclear EZ Prep Nuclei Isolation Kit Sigma NUC-101 Deposited data Raw and processed data from cell lines This paper GSE266196 Raw data from human samples This paper EGAS50000000661 Published datasets used in this study, see Table S2 N/A N/A Experimental models: Cell lines Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima CT29 Human trophoblast stem cell line Hiroaki Okae and Takahiro Arima BTS11 Oligonucleotides Btn-CTACACGACGCTCTTCCGATCTNNNNNNNNN N/A PBAT-9N-F

    Purification:

    Article Title: Clr4 SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation.
    Article Snippet: .. Total ChIP-seq read counts for defined region were analyzed using MultiBigwigSummary or MultiBamSummary. sRNA-seq For sRNA-seq, total RNAs were purified from freshly grown yeast cells using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymoresearch R2014) and sRNA were enriched using RNA Clean & Concentrator (Zymoresearch R1013). sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina (NEB E7330) and barcodedmultiplex libraries were sequenced using Illumina MiSeq platform, which generates single-end 36 nt reads. ..

    Construct:

    Article Title: Clr4 SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation.
    Article Snippet: .. Total ChIP-seq read counts for defined region were analyzed using MultiBigwigSummary or MultiBamSummary. sRNA-seq For sRNA-seq, total RNAs were purified from freshly grown yeast cells using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymoresearch R2014) and sRNA were enriched using RNA Clean & Concentrator (Zymoresearch R1013). sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina (NEB E7330) and barcodedmultiplex libraries were sequenced using Illumina MiSeq platform, which generates single-end 36 nt reads. ..



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