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35% optiprep density gradient medium cat#d1556  (Millipore)


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    Millipore 35% optiprep density gradient medium cat#d1556
    35% Optiprep Density Gradient Medium Cat#D1556, 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+medium/optiprep+gradient/pm40101718-288-53-57
    Average 90 stars, based on 1 article reviews
    35% optiprep density gradient medium cat#d1556 - by Bioz Stars, 2026-11
    90/100 stars

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    other:

    Article Title: Comparative analysis of AAV serotypes for transduction of olfactory sensory neurons
    Article Snippet: Iodixanol Gradient OptiPrepTM (Millipore Sigma D1556-250ML), or iodixanol, was purchased as a 60% (W/V) stock in water.

    Article Title: Characterization of Endogenous Retroviral-like Particles Expressed from the Spodoptera frugiperda Sf9 Cell Line.
    Article Snippet: For the OptiPrep gradient, 2 mL of 48%, 38%, 28%, 18% and 8% of OptiPrep density gradient medium (Millipore Sigma, Burlington, MA, USA; catalogue number D1556), diluted in PBS, were layered from bottom to top in an ultracentrifugation tube (Beckman Coulter, Indianapolis, IN, USA; catalogue number 344059).

    Article Title: Common AAV gene therapy vectors show nonselective transduction of ex vivo human brain tissue
    Article Snippet: OptiPrep (Millipore Sigma D1556-250ML), or iodixanol, was purchased as a 60% (W/V) stock in water; 15%, 25%, and 40% dilutions of iodixanol were made in PBS-MK (1x PBS, 1 mM MgCl 2 , 2.5 mM KCl); 2.5 μL phenol red solution (0.5% stock in PBS-MK) was added per 1 mL of iodixanol solution in the 25% and 60% fractions.

    Single Cell:


    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

    Purification:

    Article Title:
    Article Snippet: The concentrated pseudovirions were then labelled with 20uM DiO (Invitrogen) for 2 hours at room temperature in rotation. .. The labelled pseudovirions were purified using a 6%-30% OptiPrep gradient (SigmaAldrich) by centrifugation at 35,000xg for 1 hour. ..

    Centrifugation:

    Article Title:
    Article Snippet: The concentrated pseudovirions were then labelled with 20uM DiO (Invitrogen) for 2 hours at room temperature in rotation. .. The labelled pseudovirions were purified using a 6%-30% OptiPrep gradient (SigmaAldrich) by centrifugation at 35,000xg for 1 hour. ..

    Article Title: Targeting angiopoietin like-2 positive senescent cells improves cognitive impairment in adult male but not female atherosclerotic LDLr -/- ;hApoB 100 +/+ mice.
    Article Snippet: Lysis was accelerated by several freeze/thaw steps, and 1 μL of MgCl2 (1 M) in addition to benzonase (250 U/μL, #E1014, SigmaAldrich, St. Louis, MO, USA) was added per mL of lysate. .. After centrifugation, AAV1 were isolated from the supernatant by iodixanol gradients (#D1556, Sigma-Aldrich, St. Louis, MO, USA) during ultracentrifugation, then extracted with a syringe and concentrated in a phosphate-buffered saline with Tween 20 volume between 0.25 and 0.5 mL with Ultracel-100 regenerated cellulose membrane (100 kDa, #UFC910024, Millipore, St. Louis, MO, USA). .. AAV1 titration and administration in ATX mice Titration was performed by qPCR reactions using a StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA).

    Isolation:

    Article Title: Targeting angiopoietin like-2 positive senescent cells improves cognitive impairment in adult male but not female atherosclerotic LDLr -/- ;hApoB 100 +/+ mice.
    Article Snippet: Lysis was accelerated by several freeze/thaw steps, and 1 μL of MgCl2 (1 M) in addition to benzonase (250 U/μL, #E1014, SigmaAldrich, St. Louis, MO, USA) was added per mL of lysate. .. After centrifugation, AAV1 were isolated from the supernatant by iodixanol gradients (#D1556, Sigma-Aldrich, St. Louis, MO, USA) during ultracentrifugation, then extracted with a syringe and concentrated in a phosphate-buffered saline with Tween 20 volume between 0.25 and 0.5 mL with Ultracel-100 regenerated cellulose membrane (100 kDa, #UFC910024, Millipore, St. Louis, MO, USA). .. AAV1 titration and administration in ATX mice Titration was performed by qPCR reactions using a StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA).

    Saline:

    Article Title: Targeting angiopoietin like-2 positive senescent cells improves cognitive impairment in adult male but not female atherosclerotic LDLr -/- ;hApoB 100 +/+ mice.
    Article Snippet: Lysis was accelerated by several freeze/thaw steps, and 1 μL of MgCl2 (1 M) in addition to benzonase (250 U/μL, #E1014, SigmaAldrich, St. Louis, MO, USA) was added per mL of lysate. .. After centrifugation, AAV1 were isolated from the supernatant by iodixanol gradients (#D1556, Sigma-Aldrich, St. Louis, MO, USA) during ultracentrifugation, then extracted with a syringe and concentrated in a phosphate-buffered saline with Tween 20 volume between 0.25 and 0.5 mL with Ultracel-100 regenerated cellulose membrane (100 kDa, #UFC910024, Millipore, St. Louis, MO, USA). .. AAV1 titration and administration in ATX mice Titration was performed by qPCR reactions using a StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA).

    Membrane:

    Article Title: Targeting angiopoietin like-2 positive senescent cells improves cognitive impairment in adult male but not female atherosclerotic LDLr -/- ;hApoB 100 +/+ mice.
    Article Snippet: Lysis was accelerated by several freeze/thaw steps, and 1 μL of MgCl2 (1 M) in addition to benzonase (250 U/μL, #E1014, SigmaAldrich, St. Louis, MO, USA) was added per mL of lysate. .. After centrifugation, AAV1 were isolated from the supernatant by iodixanol gradients (#D1556, Sigma-Aldrich, St. Louis, MO, USA) during ultracentrifugation, then extracted with a syringe and concentrated in a phosphate-buffered saline with Tween 20 volume between 0.25 and 0.5 mL with Ultracel-100 regenerated cellulose membrane (100 kDa, #UFC910024, Millipore, St. Louis, MO, USA). .. AAV1 titration and administration in ATX mice Titration was performed by qPCR reactions using a StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA).



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    Assessment of the magnetic properties displayed by the crude cell extracts (CCEs) containing different citrine-ferritin fusion proteins using permanent neodymium ring magnets. The magnets were arranged in a 2×2 grid as shown in the leftmost panel, and covered with a black paper to aid visualization, onto which the mini petri dishes containing the CCE-OptiPrep density gradient medium mixtures (17% OptiPrep) were placed. Upon placement over the permanent magnets, the CCEs were left undisturbed for up to 69 h to follow the pattern formation. The contrast of all images was increased by 20%.

    Journal: Frontiers in Bioengineering and Biotechnology

    Article Title: Magnetic protein aggregates generated by supramolecular assembly of ferritin cages - a modular strategy for the immobilization of enzymes

    doi: 10.3389/fbioe.2024.1478198

    Figure Lengend Snippet: Assessment of the magnetic properties displayed by the crude cell extracts (CCEs) containing different citrine-ferritin fusion proteins using permanent neodymium ring magnets. The magnets were arranged in a 2×2 grid as shown in the leftmost panel, and covered with a black paper to aid visualization, onto which the mini petri dishes containing the CCE-OptiPrep density gradient medium mixtures (17% OptiPrep) were placed. Upon placement over the permanent magnets, the CCEs were left undisturbed for up to 69 h to follow the pattern formation. The contrast of all images was increased by 20%.

    Article Snippet: To visualize the magnetic properties of citrine-ferritin fusions, 5 mL of crude cell extracts (CCE) of constructs overproducing the citrine-ferritin fusions were mixed with 1 mL of OptiPrep Density Gradient Medium (STEMCELL Technologies Germany GmbH, Köln, Germany) and transferred to mini petri dishes, corresponding to 10% iodixanol (w/v) concentration in the mixture.

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