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optiprep density gradient medium  (Millipore)


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    Millipore optiprep density gradient medium
    Optiprep Density Gradient Medium, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/optiprep+density+gradient/optiprep+density+gradient+medium/pm40560236-63-1-5
    Average 90 stars, based on 1 article reviews
    optiprep density gradient medium - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Transfection:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Centrifugation:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Bioprocessing:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Isolation:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Article Title: PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis.
    Article Snippet: .. Primary cell isolation and cell culture Mouse hepatic stellate cells (HSCs) were isolated as previously described.3,9,11 Briefly, livers were perfused with HBSS containing collagenase and pronase via the portal vein prior to mechanical disruption of tissue and isolation of HSCs via an Optiprep density gradient (Sigma). ..

    Sterility:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Filtration:

    Article Title: Astrocytic polyamine transport by ATP13A4 tunes excitatory synaptic transmission
    Article Snippet: pZac2.1-GfaABC1D-Lamp1-TurboID-HA was generated by amplifying Lamp1 via PCR from the plasmid pmCherry-Lysosomes-20 (RRID:Addgene_55073) using primers (F): 5’-AGGCTAGCCGCCACCATGGCGGCCCCGGGCGCCCGGCGGC-3’; and (R): 5’-GAGCTCGAGGGTGGCGACCGGTGGATCCGCG-3’). .. Three days after transfection, cells were collected in 15 mM NaCl, 5 mM Tris-HCl, pH 8.5, and lysed with repeat freeze-thaw cycles followed by treatment with Benzonase (Novagen, Cat# 70664) at 37 °C for 30 min. Lysed cells were pelleted by centrifugation, and the supernatant, containing AAVs, was applied to an OptiPrep density gradient (15%, 25%, 40%, and 60%; Sigma, Cat# D1556) and centrifuged at 67,000 rpm using a Beckman Ti-70 rotor for 1 h. The AAV-enriched fraction was isolated from between 40% and 60% iodixanol solution and concentrated by repeated washes with sterile PBS in an Amicon Ultra-15 filtration unit (100 kDa MWCO; Millipore, Cat# UFC910008) to a final volume of ∼100 μL and aliquoted for storage at −80 °C. ..

    Cell Isolation:

    Article Title: PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis.
    Article Snippet: .. Primary cell isolation and cell culture Mouse hepatic stellate cells (HSCs) were isolated as previously described.3,9,11 Briefly, livers were perfused with HBSS containing collagenase and pronase via the portal vein prior to mechanical disruption of tissue and isolation of HSCs via an Optiprep density gradient (Sigma). ..

    Cell Culture:

    Article Title: PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis.
    Article Snippet: .. Primary cell isolation and cell culture Mouse hepatic stellate cells (HSCs) were isolated as previously described.3,9,11 Briefly, livers were perfused with HBSS containing collagenase and pronase via the portal vein prior to mechanical disruption of tissue and isolation of HSCs via an Optiprep density gradient (Sigma). ..

    Disruption:

    Article Title: PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis.
    Article Snippet: .. Primary cell isolation and cell culture Mouse hepatic stellate cells (HSCs) were isolated as previously described.3,9,11 Briefly, livers were perfused with HBSS containing collagenase and pronase via the portal vein prior to mechanical disruption of tissue and isolation of HSCs via an Optiprep density gradient (Sigma). ..

    Recombinant:

    Article Title: Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MeCP2 (clone D4F3) Cell Signaling Technology #3456; RRID: AB_2143894 Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) Cell Signaling Technology #9733; RRID: AB_2616029 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) Cell Signaling Technology #8173; RRID: AB_10949503 Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] Abcam #ab8898; RRID: AB_306848 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) Cell Signaling Technology #9649; RRID: AB_823528 Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) Abcam #ab78517; RRID: AB_1951279 Rabbit polyclonal IgG Millipore #12-370; RRID: AB_145841 Mouse monoclonal anti-Vinculin (clone hVIN-1) MilliporeSigma #V9131; RRID: AB_477629 Mouse monoclonal anti-GAPDH (clone 6C5) Advanced ImmunoChemical Inc. #2-RGM2; RRID: AB_2721282 Chicken polyclonal anti-alpha tubulin Abcam #ab89984; RRID: AB_10672056 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma-Aldrich #T5648 Peanut oil Sigma-Aldrich #P2144 OptiPrep density gradient Sigma-Aldrich #D15556 Spermidine Sigma-Aldrich #S0266 Ultrapure BSA Invitrogen #AM2618 cOmplete protease inhibitor Roche #11873580001 Digitonin Calbiochem #11024-24-1 pAG-MNase Epicypher #15-1016 Critical commercial assays Qiagen miRNeasy Mini Qiagen #217004 Qiagen RNase free DNase Qiagen #79254 NEB Next II DNA Ultra Kit New England Biolabs #E7645S Unique Combinatorial Dual index kit New England Biolabs #E6440S, #E6442S, #E6444S Deposited data Mecp2 Adult Knockout RNA-seq (raw and processed) This study GEO: GSE246119 Mecp2 Adult Knockout CUT&RUN (raw and processed) This study GEO: GSE246664 Mecp2-G118E RNA-seq (raw and processed) This study GEO: GSE277077 Mecp2-null Cortex RNA-seq Zhou et al.36 GEO: GSE179229 Mecp2-null Cortex RNA-seq Clemens et al.10 GEO: GSE123372 Mecp2-null Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-R306C Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-null Hypothalamus RNA-seq Chen et al.20 GEO: GSE66870 Mecp2-null Cerebellum RNA-seq Raman et al.37 GEO: GSE105045 Reduced representation bisulfite sequencing of hippocampus Reizel et al.39 GEO: GSE85251 Hippocampal RNA-seq used in deconvolution Habib et al.64 GEO: GSE143758 Hippocampal RNA-seq used in deconvolution Methi et al.65 GEO: GSE234278 (Continued on next page) Neuron 113, 1–16.e1–e8, February 5, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains B6.129S4(C)-Mecp2tm1Jae/Mmucd MMRCC MMRCC# 011918-UCD; RRID: MMRRC_011918-UCD B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J The Jackson Labs Jax #007001; RRID: IMSR_JAX:007001 Mecp2-G118E Zhou et al.36 N/A C57BL6/J The Jackson Labs Jax #000664; RRID: IMSR_JAX:000664 Oligonucleotides Ppia qPCR forward primer This paper N/A Ppia qPCR reverse primer This paper N/A Mecp2 qPCR forward primer This paper N/A Mecp2 qPCR reverse primer This paper N/A Software and algorithms STAR aligner Dobin et al.66 https://github.com/alexdobin/STAR DESeq2 Love et al.67 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CIBERSORTx Newman et al.68 https://cibersortx.stanford.edu/ Bismark Krueger and Andrews69 https://github.com/FelixKrueger/Bismark samtools Li et al.70 https://www.htslib.org/ Trimmomatic Bolger et al.71 http://www.usadellab.org/cms/?page= trimmomatic Trimgalore N/A https://github.com/FelixKrueger/TrimGalore bedtools Quinlan and Hall72 https://bedtools.readthedocs.io/en/latest/ MACS2 Zhang et al.73 https://pypi.org/project/MACS2/ edgeR Robinson et al.74 https://bioconductor.org/packages/ release/bioc/html/edgeR.html deepTools Ramirez et al.75 https://deeptools.readthedocs.io/en/develop/ Other Concavalin A magnetic beads Bangs Laboratories Inc. #BP531 SPRI select beads Beckman Coulter #B23318 E. coli spike in Epicypher #18-1401

    Protease Inhibitor:

    Article Title: Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MeCP2 (clone D4F3) Cell Signaling Technology #3456; RRID: AB_2143894 Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) Cell Signaling Technology #9733; RRID: AB_2616029 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) Cell Signaling Technology #8173; RRID: AB_10949503 Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] Abcam #ab8898; RRID: AB_306848 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) Cell Signaling Technology #9649; RRID: AB_823528 Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) Abcam #ab78517; RRID: AB_1951279 Rabbit polyclonal IgG Millipore #12-370; RRID: AB_145841 Mouse monoclonal anti-Vinculin (clone hVIN-1) MilliporeSigma #V9131; RRID: AB_477629 Mouse monoclonal anti-GAPDH (clone 6C5) Advanced ImmunoChemical Inc. #2-RGM2; RRID: AB_2721282 Chicken polyclonal anti-alpha tubulin Abcam #ab89984; RRID: AB_10672056 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma-Aldrich #T5648 Peanut oil Sigma-Aldrich #P2144 OptiPrep density gradient Sigma-Aldrich #D15556 Spermidine Sigma-Aldrich #S0266 Ultrapure BSA Invitrogen #AM2618 cOmplete protease inhibitor Roche #11873580001 Digitonin Calbiochem #11024-24-1 pAG-MNase Epicypher #15-1016 Critical commercial assays Qiagen miRNeasy Mini Qiagen #217004 Qiagen RNase free DNase Qiagen #79254 NEB Next II DNA Ultra Kit New England Biolabs #E7645S Unique Combinatorial Dual index kit New England Biolabs #E6440S, #E6442S, #E6444S Deposited data Mecp2 Adult Knockout RNA-seq (raw and processed) This study GEO: GSE246119 Mecp2 Adult Knockout CUT&RUN (raw and processed) This study GEO: GSE246664 Mecp2-G118E RNA-seq (raw and processed) This study GEO: GSE277077 Mecp2-null Cortex RNA-seq Zhou et al.36 GEO: GSE179229 Mecp2-null Cortex RNA-seq Clemens et al.10 GEO: GSE123372 Mecp2-null Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-R306C Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-null Hypothalamus RNA-seq Chen et al.20 GEO: GSE66870 Mecp2-null Cerebellum RNA-seq Raman et al.37 GEO: GSE105045 Reduced representation bisulfite sequencing of hippocampus Reizel et al.39 GEO: GSE85251 Hippocampal RNA-seq used in deconvolution Habib et al.64 GEO: GSE143758 Hippocampal RNA-seq used in deconvolution Methi et al.65 GEO: GSE234278 (Continued on next page) Neuron 113, 1–16.e1–e8, February 5, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains B6.129S4(C)-Mecp2tm1Jae/Mmucd MMRCC MMRCC# 011918-UCD; RRID: MMRRC_011918-UCD B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J The Jackson Labs Jax #007001; RRID: IMSR_JAX:007001 Mecp2-G118E Zhou et al.36 N/A C57BL6/J The Jackson Labs Jax #000664; RRID: IMSR_JAX:000664 Oligonucleotides Ppia qPCR forward primer This paper N/A Ppia qPCR reverse primer This paper N/A Mecp2 qPCR forward primer This paper N/A Mecp2 qPCR reverse primer This paper N/A Software and algorithms STAR aligner Dobin et al.66 https://github.com/alexdobin/STAR DESeq2 Love et al.67 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CIBERSORTx Newman et al.68 https://cibersortx.stanford.edu/ Bismark Krueger and Andrews69 https://github.com/FelixKrueger/Bismark samtools Li et al.70 https://www.htslib.org/ Trimmomatic Bolger et al.71 http://www.usadellab.org/cms/?page= trimmomatic Trimgalore N/A https://github.com/FelixKrueger/TrimGalore bedtools Quinlan and Hall72 https://bedtools.readthedocs.io/en/latest/ MACS2 Zhang et al.73 https://pypi.org/project/MACS2/ edgeR Robinson et al.74 https://bioconductor.org/packages/ release/bioc/html/edgeR.html deepTools Ramirez et al.75 https://deeptools.readthedocs.io/en/develop/ Other Concavalin A magnetic beads Bangs Laboratories Inc. #BP531 SPRI select beads Beckman Coulter #B23318 E. coli spike in Epicypher #18-1401

    Knock-Out:

    Article Title: Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MeCP2 (clone D4F3) Cell Signaling Technology #3456; RRID: AB_2143894 Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) Cell Signaling Technology #9733; RRID: AB_2616029 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) Cell Signaling Technology #8173; RRID: AB_10949503 Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] Abcam #ab8898; RRID: AB_306848 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) Cell Signaling Technology #9649; RRID: AB_823528 Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) Abcam #ab78517; RRID: AB_1951279 Rabbit polyclonal IgG Millipore #12-370; RRID: AB_145841 Mouse monoclonal anti-Vinculin (clone hVIN-1) MilliporeSigma #V9131; RRID: AB_477629 Mouse monoclonal anti-GAPDH (clone 6C5) Advanced ImmunoChemical Inc. #2-RGM2; RRID: AB_2721282 Chicken polyclonal anti-alpha tubulin Abcam #ab89984; RRID: AB_10672056 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma-Aldrich #T5648 Peanut oil Sigma-Aldrich #P2144 OptiPrep density gradient Sigma-Aldrich #D15556 Spermidine Sigma-Aldrich #S0266 Ultrapure BSA Invitrogen #AM2618 cOmplete protease inhibitor Roche #11873580001 Digitonin Calbiochem #11024-24-1 pAG-MNase Epicypher #15-1016 Critical commercial assays Qiagen miRNeasy Mini Qiagen #217004 Qiagen RNase free DNase Qiagen #79254 NEB Next II DNA Ultra Kit New England Biolabs #E7645S Unique Combinatorial Dual index kit New England Biolabs #E6440S, #E6442S, #E6444S Deposited data Mecp2 Adult Knockout RNA-seq (raw and processed) This study GEO: GSE246119 Mecp2 Adult Knockout CUT&RUN (raw and processed) This study GEO: GSE246664 Mecp2-G118E RNA-seq (raw and processed) This study GEO: GSE277077 Mecp2-null Cortex RNA-seq Zhou et al.36 GEO: GSE179229 Mecp2-null Cortex RNA-seq Clemens et al.10 GEO: GSE123372 Mecp2-null Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-R306C Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-null Hypothalamus RNA-seq Chen et al.20 GEO: GSE66870 Mecp2-null Cerebellum RNA-seq Raman et al.37 GEO: GSE105045 Reduced representation bisulfite sequencing of hippocampus Reizel et al.39 GEO: GSE85251 Hippocampal RNA-seq used in deconvolution Habib et al.64 GEO: GSE143758 Hippocampal RNA-seq used in deconvolution Methi et al.65 GEO: GSE234278 (Continued on next page) Neuron 113, 1–16.e1–e8, February 5, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains B6.129S4(C)-Mecp2tm1Jae/Mmucd MMRCC MMRCC# 011918-UCD; RRID: MMRRC_011918-UCD B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J The Jackson Labs Jax #007001; RRID: IMSR_JAX:007001 Mecp2-G118E Zhou et al.36 N/A C57BL6/J The Jackson Labs Jax #000664; RRID: IMSR_JAX:000664 Oligonucleotides Ppia qPCR forward primer This paper N/A Ppia qPCR reverse primer This paper N/A Mecp2 qPCR forward primer This paper N/A Mecp2 qPCR reverse primer This paper N/A Software and algorithms STAR aligner Dobin et al.66 https://github.com/alexdobin/STAR DESeq2 Love et al.67 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CIBERSORTx Newman et al.68 https://cibersortx.stanford.edu/ Bismark Krueger and Andrews69 https://github.com/FelixKrueger/Bismark samtools Li et al.70 https://www.htslib.org/ Trimmomatic Bolger et al.71 http://www.usadellab.org/cms/?page= trimmomatic Trimgalore N/A https://github.com/FelixKrueger/TrimGalore bedtools Quinlan and Hall72 https://bedtools.readthedocs.io/en/latest/ MACS2 Zhang et al.73 https://pypi.org/project/MACS2/ edgeR Robinson et al.74 https://bioconductor.org/packages/ release/bioc/html/edgeR.html deepTools Ramirez et al.75 https://deeptools.readthedocs.io/en/develop/ Other Concavalin A magnetic beads Bangs Laboratories Inc. #BP531 SPRI select beads Beckman Coulter #B23318 E. coli spike in Epicypher #18-1401

    RNA Sequencing:

    Article Title: Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MeCP2 (clone D4F3) Cell Signaling Technology #3456; RRID: AB_2143894 Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) Cell Signaling Technology #9733; RRID: AB_2616029 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) Cell Signaling Technology #8173; RRID: AB_10949503 Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] Abcam #ab8898; RRID: AB_306848 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) Cell Signaling Technology #9649; RRID: AB_823528 Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) Abcam #ab78517; RRID: AB_1951279 Rabbit polyclonal IgG Millipore #12-370; RRID: AB_145841 Mouse monoclonal anti-Vinculin (clone hVIN-1) MilliporeSigma #V9131; RRID: AB_477629 Mouse monoclonal anti-GAPDH (clone 6C5) Advanced ImmunoChemical Inc. #2-RGM2; RRID: AB_2721282 Chicken polyclonal anti-alpha tubulin Abcam #ab89984; RRID: AB_10672056 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma-Aldrich #T5648 Peanut oil Sigma-Aldrich #P2144 OptiPrep density gradient Sigma-Aldrich #D15556 Spermidine Sigma-Aldrich #S0266 Ultrapure BSA Invitrogen #AM2618 cOmplete protease inhibitor Roche #11873580001 Digitonin Calbiochem #11024-24-1 pAG-MNase Epicypher #15-1016 Critical commercial assays Qiagen miRNeasy Mini Qiagen #217004 Qiagen RNase free DNase Qiagen #79254 NEB Next II DNA Ultra Kit New England Biolabs #E7645S Unique Combinatorial Dual index kit New England Biolabs #E6440S, #E6442S, #E6444S Deposited data Mecp2 Adult Knockout RNA-seq (raw and processed) This study GEO: GSE246119 Mecp2 Adult Knockout CUT&RUN (raw and processed) This study GEO: GSE246664 Mecp2-G118E RNA-seq (raw and processed) This study GEO: GSE277077 Mecp2-null Cortex RNA-seq Zhou et al.36 GEO: GSE179229 Mecp2-null Cortex RNA-seq Clemens et al.10 GEO: GSE123372 Mecp2-null Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-R306C Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-null Hypothalamus RNA-seq Chen et al.20 GEO: GSE66870 Mecp2-null Cerebellum RNA-seq Raman et al.37 GEO: GSE105045 Reduced representation bisulfite sequencing of hippocampus Reizel et al.39 GEO: GSE85251 Hippocampal RNA-seq used in deconvolution Habib et al.64 GEO: GSE143758 Hippocampal RNA-seq used in deconvolution Methi et al.65 GEO: GSE234278 (Continued on next page) Neuron 113, 1–16.e1–e8, February 5, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains B6.129S4(C)-Mecp2tm1Jae/Mmucd MMRCC MMRCC# 011918-UCD; RRID: MMRRC_011918-UCD B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J The Jackson Labs Jax #007001; RRID: IMSR_JAX:007001 Mecp2-G118E Zhou et al.36 N/A C57BL6/J The Jackson Labs Jax #000664; RRID: IMSR_JAX:000664 Oligonucleotides Ppia qPCR forward primer This paper N/A Ppia qPCR reverse primer This paper N/A Mecp2 qPCR forward primer This paper N/A Mecp2 qPCR reverse primer This paper N/A Software and algorithms STAR aligner Dobin et al.66 https://github.com/alexdobin/STAR DESeq2 Love et al.67 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CIBERSORTx Newman et al.68 https://cibersortx.stanford.edu/ Bismark Krueger and Andrews69 https://github.com/FelixKrueger/Bismark samtools Li et al.70 https://www.htslib.org/ Trimmomatic Bolger et al.71 http://www.usadellab.org/cms/?page= trimmomatic Trimgalore N/A https://github.com/FelixKrueger/TrimGalore bedtools Quinlan and Hall72 https://bedtools.readthedocs.io/en/latest/ MACS2 Zhang et al.73 https://pypi.org/project/MACS2/ edgeR Robinson et al.74 https://bioconductor.org/packages/ release/bioc/html/edgeR.html deepTools Ramirez et al.75 https://deeptools.readthedocs.io/en/develop/ Other Concavalin A magnetic beads Bangs Laboratories Inc. #BP531 SPRI select beads Beckman Coulter #B23318 E. coli spike in Epicypher #18-1401

    Methylation Sequencing:

    Article Title: Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MeCP2 (clone D4F3) Cell Signaling Technology #3456; RRID: AB_2143894 Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) Cell Signaling Technology #9733; RRID: AB_2616029 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) Cell Signaling Technology #8173; RRID: AB_10949503 Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] Abcam #ab8898; RRID: AB_306848 Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) Cell Signaling Technology #9649; RRID: AB_823528 Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) Abcam #ab78517; RRID: AB_1951279 Rabbit polyclonal IgG Millipore #12-370; RRID: AB_145841 Mouse monoclonal anti-Vinculin (clone hVIN-1) MilliporeSigma #V9131; RRID: AB_477629 Mouse monoclonal anti-GAPDH (clone 6C5) Advanced ImmunoChemical Inc. #2-RGM2; RRID: AB_2721282 Chicken polyclonal anti-alpha tubulin Abcam #ab89984; RRID: AB_10672056 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma-Aldrich #T5648 Peanut oil Sigma-Aldrich #P2144 OptiPrep density gradient Sigma-Aldrich #D15556 Spermidine Sigma-Aldrich #S0266 Ultrapure BSA Invitrogen #AM2618 cOmplete protease inhibitor Roche #11873580001 Digitonin Calbiochem #11024-24-1 pAG-MNase Epicypher #15-1016 Critical commercial assays Qiagen miRNeasy Mini Qiagen #217004 Qiagen RNase free DNase Qiagen #79254 NEB Next II DNA Ultra Kit New England Biolabs #E7645S Unique Combinatorial Dual index kit New England Biolabs #E6440S, #E6442S, #E6444S Deposited data Mecp2 Adult Knockout RNA-seq (raw and processed) This study GEO: GSE246119 Mecp2 Adult Knockout CUT&RUN (raw and processed) This study GEO: GSE246664 Mecp2-G118E RNA-seq (raw and processed) This study GEO: GSE277077 Mecp2-null Cortex RNA-seq Zhou et al.36 GEO: GSE179229 Mecp2-null Cortex RNA-seq Clemens et al.10 GEO: GSE123372 Mecp2-null Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-R306C Cortex RNA-seq Boxer et al.9 GEO: GSE128178 Mecp2-null Hypothalamus RNA-seq Chen et al.20 GEO: GSE66870 Mecp2-null Cerebellum RNA-seq Raman et al.37 GEO: GSE105045 Reduced representation bisulfite sequencing of hippocampus Reizel et al.39 GEO: GSE85251 Hippocampal RNA-seq used in deconvolution Habib et al.64 GEO: GSE143758 Hippocampal RNA-seq used in deconvolution Methi et al.65 GEO: GSE234278 (Continued on next page) Neuron 113, 1–16.e1–e8, February 5, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains B6.129S4(C)-Mecp2tm1Jae/Mmucd MMRCC MMRCC# 011918-UCD; RRID: MMRRC_011918-UCD B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J The Jackson Labs Jax #007001; RRID: IMSR_JAX:007001 Mecp2-G118E Zhou et al.36 N/A C57BL6/J The Jackson Labs Jax #000664; RRID: IMSR_JAX:000664 Oligonucleotides Ppia qPCR forward primer This paper N/A Ppia qPCR reverse primer This paper N/A Mecp2 qPCR forward primer This paper N/A Mecp2 qPCR reverse primer This paper N/A Software and algorithms STAR aligner Dobin et al.66 https://github.com/alexdobin/STAR DESeq2 Love et al.67 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CIBERSORTx Newman et al.68 https://cibersortx.stanford.edu/ Bismark Krueger and Andrews69 https://github.com/FelixKrueger/Bismark samtools Li et al.70 https://www.htslib.org/ Trimmomatic Bolger et al.71 http://www.usadellab.org/cms/?page= trimmomatic Trimgalore N/A https://github.com/FelixKrueger/TrimGalore bedtools Quinlan and Hall72 https://bedtools.readthedocs.io/en/latest/ MACS2 Zhang et al.73 https://pypi.org/project/MACS2/ edgeR Robinson et al.74 https://bioconductor.org/packages/ release/bioc/html/edgeR.html deepTools Ramirez et al.75 https://deeptools.readthedocs.io/en/develop/ Other Concavalin A magnetic beads Bangs Laboratories Inc. #BP531 SPRI select beads Beckman Coulter #B23318 E. coli spike in Epicypher #18-1401

    other:

    Article Title: Proteomic profiling of tumour tissue‐derived extracellular vesicles in colon cancer
    Article Snippet: The two pellets enriched for large and small EVs were pooled, and the EVs were further purified by a bottom‐loaded iodixanol density cushion (Optiprep density gradient, Sigma Aldrich).



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