Magnetic Beads:Article Title: DLX2 acts as a pioneer factor and drives Msx1 + ectomesenchyme formation from embryonic stem cells
Article Snippet: Protein concentrations were quantified by bicinchoninic acid (BCA) assay (Thermo Fisher Scientific, catalog no. A65453), and 700 μg of protein per sample was diluted to 500 μl. .. After preclearing with magnetic beads, the lysates were incubated overnight at 4°C with anti-FLAG, anti-pan LAP2, anti-H3K27ac, or control IgG antibodies, followed by a 4-hour incubation with Protein G or Protein A/G magnetic beads (Invitrogen, catalog no. 10004D; MedChemExpress, catalog no. HY-K0202). .. Total proteins were extracted using NP-40 lysis buffer (Beyotime, catalog no. P0013F) supplemented with a protease inhibitor cocktail (MedChemExpress, catalog no. HY-K0010), incubated on ice for 30 min, and centrifuged at 12,000 g for 30 min at 4°C.
Incubation:Article Title: DLX2 acts as a pioneer factor and drives Msx1 + ectomesenchyme formation from embryonic stem cells
Article Snippet: Protein concentrations were quantified by bicinchoninic acid (BCA) assay (Thermo Fisher Scientific, catalog no. A65453), and 700 μg of protein per sample was diluted to 500 μl. .. After preclearing with magnetic beads, the lysates were incubated overnight at 4°C with anti-FLAG, anti-pan LAP2, anti-H3K27ac, or control IgG antibodies, followed by a 4-hour incubation with Protein G or Protein A/G magnetic beads (Invitrogen, catalog no. 10004D; MedChemExpress, catalog no. HY-K0202). .. Total proteins were extracted using NP-40 lysis buffer (Beyotime, catalog no. P0013F) supplemented with a protease inhibitor cocktail (MedChemExpress, catalog no. HY-K0010), incubated on ice for 30 min, and centrifuged at 12,000 g for 30 min at 4°C.
Control:Article Title: DLX2 acts as a pioneer factor and drives Msx1 + ectomesenchyme formation from embryonic stem cells
Article Snippet: Protein concentrations were quantified by bicinchoninic acid (BCA) assay (Thermo Fisher Scientific, catalog no. A65453), and 700 μg of protein per sample was diluted to 500 μl. .. After preclearing with magnetic beads, the lysates were incubated overnight at 4°C with anti-FLAG, anti-pan LAP2, anti-H3K27ac, or control IgG antibodies, followed by a 4-hour incubation with Protein G or Protein A/G magnetic beads (Invitrogen, catalog no. 10004D; MedChemExpress, catalog no. HY-K0202). .. Total proteins were extracted using NP-40 lysis buffer (Beyotime, catalog no. P0013F) supplemented with a protease inhibitor cocktail (MedChemExpress, catalog no. HY-K0010), incubated on ice for 30 min, and centrifuged at 12,000 g for 30 min at 4°C.
Methylation:Article Title: Rank signaling drives basal cell-lineage infidelity leading to mammary tumorigenesis.
Article Snippet: .. For modulating the epigenome (by targeting H3K27 methylation), 4-week-old mice were treated intraperitoneally 3 times per week during 5 weeks with 50 mg/kg of the EZH2 inhibitor GSK-126 (MedChemExpress, HY-13470-50 MG) or the KDM6 inhibitor GSK-J4 (MedChemExpress, HY-15648B-50 MG) dissolved in DMSO/Captisol (Selleck Chemicals, S4592-5G). .. Mammary tumors were induced by MPA and 7,12- dimethylbenzanthracene (DMBA) (Fisher Scientific #408181000) as described in 14,24.
Recombinant:Article Title: Acetylation at lysine 27 on maternal H3.3 regulates minor zygotic genome activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Recombinant anti-H3.3 Active Motif Cat# 91191; RRID: AB_2793796 Rabbit polyclonal anti-H3 Abcam Cat# ab1791; RRID: AB_302613 Rabbit Monoclonal anti-H3.3S31ph Abcam Cat# ab92628; RRID: AB_10563637 Rabbit Polyclonal anti-H3K27ac Active Motif Cat# 39133; RRID: AB_2561016 Rabbit monoclonal anti-HA-Tag CST Cat# 3724; RRID: AB_1549585 Chemicals, peptides, and recombinant proteins SB-218078 MCE HY-107407 Recombinant Histone H3.3 Active Motif Cat# 31295 Micrococcal Nuclease NEB M0247S dsDNA Fragmentase NEB M0348S Poly(ethylene glycol) Sigma-Aldrich 81255-250G Triton X-100 Sigma-Aldrich 93443-100ML TWEEN 20 Sigma-Aldrich P1379 Phenol:Chloroform:Isoamyl Alcohol Sigma-Aldrich P3803-100ML Glycogen Sigma-Aldrich 10901393001 Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Sodium dodecyl sulfate Sigma-Aldrich 71736-100ML Magnesium chloride Sigma-Aldrich M1028-10X1ML PMSF Sigma-Aldrich 93482-50ML-F Glycine Sigma-Aldrich G7126-10MG Sodium chloride Sigma-Aldrich S6546-1L PMSG Sigma-Aldrich G4527 hCG Sigma-Aldrich CG10-1VL Milrinone Sigma-Aldrich 475840 CZB Medium Sigma-Aldrich MR-019 Cytochalasin B Sigma-Aldrich C6762 Strontium chloride Sigma-Aldrich 439665 Dynabeads Protein A Thermo Fisher 10001D Formaldehyde Thermo Fisher BP531-500 FastDigest SmiI Thermo Fisher FD1244 Fixative Solutions Thermo Fisher FB002 EDTA, pH8.0 Beyotime ST066 1M Tris-HCl, pH8.0 Beyotime ST787 RIPA Beyotime P0013B NP-40 Beyotime ST366 3M NaAc Beyotime ST351 MaXtract High Density QIAGEN 129046 AMPure XP Beckman A63881 DTT Abcam ab141390 DNA Clean Beads Vazyme N411 KSOM Merck MR-121-D M2 medium Merck M7167 G-1 plus medium Vitrolife Cat#10128 (Continued on next page) 12 Cell Reports 44, 115148, January 28, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays HiScribe T7 ARCA mRNA Kit NEB E2060S KAPA HyperPrep Kit Roche kk8504 KAPA Single-Indexed Adapter Kit Roche Kk8700 NGS End Repair/dA-Tailing Module Yeasen 12608ES96 Single Cell Full Length mRNA-Amplification Kit Vazyme N712 Hyperactive Universal CUT&Tag Assay Kit Vazyme TD903 TruePrep DNA Library Prep Kit Vazyme TD501 Deposited data ChIP-seq, CUT&tag and RNA-seq data This study GSE242960 H3K27ac ChIP-seq Li et al.13 GSE185653 Allelic H3K27ac ChIP-seq Wang et al.11 GSE207222 H3K36me3 Xu et al.38 GSE112834 H3K4me3 and H3K27me3 Liu et al.39 GSE73952 H3K9me3 Wang et al.40 GSE98149 H3-sperm Jung et al.41 GSE79227 ATAC-seq Wu et al.42 GSE66390 ZGA genes Park et al.43 DRA001066 Experimental models: Organisms/strains H3.3B-HA reporter mice In-house44 N/A ICR mice Charles River RRID: IMSR_CRL:022 B6D2F1 The Jackson Laboratory #100006 - B6D2F1/J Oligonucleotides Morpholinos, siRNAs.
Protease Inhibitor:Article Title: Acetylation at lysine 27 on maternal H3.3 regulates minor zygotic genome activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Recombinant anti-H3.3 Active Motif Cat# 91191; RRID: AB_2793796 Rabbit polyclonal anti-H3 Abcam Cat# ab1791; RRID: AB_302613 Rabbit Monoclonal anti-H3.3S31ph Abcam Cat# ab92628; RRID: AB_10563637 Rabbit Polyclonal anti-H3K27ac Active Motif Cat# 39133; RRID: AB_2561016 Rabbit monoclonal anti-HA-Tag CST Cat# 3724; RRID: AB_1549585 Chemicals, peptides, and recombinant proteins SB-218078 MCE HY-107407 Recombinant Histone H3.3 Active Motif Cat# 31295 Micrococcal Nuclease NEB M0247S dsDNA Fragmentase NEB M0348S Poly(ethylene glycol) Sigma-Aldrich 81255-250G Triton X-100 Sigma-Aldrich 93443-100ML TWEEN 20 Sigma-Aldrich P1379 Phenol:Chloroform:Isoamyl Alcohol Sigma-Aldrich P3803-100ML Glycogen Sigma-Aldrich 10901393001 Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Sodium dodecyl sulfate Sigma-Aldrich 71736-100ML Magnesium chloride Sigma-Aldrich M1028-10X1ML PMSF Sigma-Aldrich 93482-50ML-F Glycine Sigma-Aldrich G7126-10MG Sodium chloride Sigma-Aldrich S6546-1L PMSG Sigma-Aldrich G4527 hCG Sigma-Aldrich CG10-1VL Milrinone Sigma-Aldrich 475840 CZB Medium Sigma-Aldrich MR-019 Cytochalasin B Sigma-Aldrich C6762 Strontium chloride Sigma-Aldrich 439665 Dynabeads Protein A Thermo Fisher 10001D Formaldehyde Thermo Fisher BP531-500 FastDigest SmiI Thermo Fisher FD1244 Fixative Solutions Thermo Fisher FB002 EDTA, pH8.0 Beyotime ST066 1M Tris-HCl, pH8.0 Beyotime ST787 RIPA Beyotime P0013B NP-40 Beyotime ST366 3M NaAc Beyotime ST351 MaXtract High Density QIAGEN 129046 AMPure XP Beckman A63881 DTT Abcam ab141390 DNA Clean Beads Vazyme N411 KSOM Merck MR-121-D M2 medium Merck M7167 G-1 plus medium Vitrolife Cat#10128 (Continued on next page) 12 Cell Reports 44, 115148, January 28, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays HiScribe T7 ARCA mRNA Kit NEB E2060S KAPA HyperPrep Kit Roche kk8504 KAPA Single-Indexed Adapter Kit Roche Kk8700 NGS End Repair/dA-Tailing Module Yeasen 12608ES96 Single Cell Full Length mRNA-Amplification Kit Vazyme N712 Hyperactive Universal CUT&Tag Assay Kit Vazyme TD903 TruePrep DNA Library Prep Kit Vazyme TD501 Deposited data ChIP-seq, CUT&tag and RNA-seq data This study GSE242960 H3K27ac ChIP-seq Li et al.13 GSE185653 Allelic H3K27ac ChIP-seq Wang et al.11 GSE207222 H3K36me3 Xu et al.38 GSE112834 H3K4me3 and H3K27me3 Liu et al.39 GSE73952 H3K9me3 Wang et al.40 GSE98149 H3-sperm Jung et al.41 GSE79227 ATAC-seq Wu et al.42 GSE66390 ZGA genes Park et al.43 DRA001066 Experimental models: Organisms/strains H3.3B-HA reporter mice In-house44 N/A ICR mice Charles River RRID: IMSR_CRL:022 B6D2F1 The Jackson Laboratory #100006 - B6D2F1/J Oligonucleotides Morpholinos, siRNAs.
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