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  • 92
    ATCC methylophilus methylotrophus atcc 53528
    16S rDNA similarities, digital DNA–DNA hybridization, and proportions of shared protein-coding genes (⩾70% protein similarity) of the two strains and different members of Methylophilaceae
    Methylophilus Methylotrophus Atcc 53528, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/methylophilus methylotrophus atcc 53528/product/ATCC
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    methylophilus methylotrophus atcc 53528 - by Bioz Stars, 2024-05
    92/100 stars
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    85
    DSMZ sorangium cellulosum
    16S rDNA similarities, digital DNA–DNA hybridization, and proportions of shared protein-coding genes (⩾70% protein similarity) of the two strains and different members of Methylophilaceae
    Sorangium Cellulosum, supplied by DSMZ, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sorangium cellulosum/product/DSMZ
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    sorangium cellulosum - by Bioz Stars, 2024-05
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    93
    Cell Signaling Technology Inc rabbit anti human foxa1 monoclonal antibody
    (a) Schematic of experimental design to infect K562 cells with <t>FoxA1-</t> or Hnf4a-lentivirus and then perform functional assays on dox-induced cells. In CUT&Tag, a protein A-protein G fusion (pA/G) increases the binding spectrum for Fc-binding and allows Tn5 recruitment to antibody-labeled TF binding sites. In ATAC-seq, Tn5 homes to any accessible site. And in RNA-seq, polyA RNA is captured and sequenced. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1-Hnf4a compared to the number actually activated. Both liver-( P < 10 −38 ) and intestinal-enrichment ( P < 10 −13 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) Genome browser view of a representative liver-specific locus ( ALB ) in FoxA1-Hnf4a clonal line that shows uninduced and induced accessibility, FoxA1 binding, and Hnf4a binding. (d) Meta plot showing uninduced and induced accessibility at all FoxA1-Hnf4a co-bound sites within 50 kb of each FoxA1-Hnf4a activated liver-specific gene (n = 53).
    Rabbit Anti Human Foxa1 Monoclonal Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti human foxa1 monoclonal antibody/product/Cell Signaling Technology Inc
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    80
    BOC Sciences human growth hormone
    (a) Schematic of experimental design to infect K562 cells with <t>FoxA1-</t> or Hnf4a-lentivirus and then perform functional assays on dox-induced cells. In CUT&Tag, a protein A-protein G fusion (pA/G) increases the binding spectrum for Fc-binding and allows Tn5 recruitment to antibody-labeled TF binding sites. In ATAC-seq, Tn5 homes to any accessible site. And in RNA-seq, polyA RNA is captured and sequenced. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1-Hnf4a compared to the number actually activated. Both liver-( P < 10 −38 ) and intestinal-enrichment ( P < 10 −13 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) Genome browser view of a representative liver-specific locus ( ALB ) in FoxA1-Hnf4a clonal line that shows uninduced and induced accessibility, FoxA1 binding, and Hnf4a binding. (d) Meta plot showing uninduced and induced accessibility at all FoxA1-Hnf4a co-bound sites within 50 kb of each FoxA1-Hnf4a activated liver-specific gene (n = 53).
    Human Growth Hormone, supplied by BOC Sciences, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human growth hormone/product/BOC Sciences
    Average 80 stars, based on 1 article reviews
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    human growth hormone - by Bioz Stars, 2024-05
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    N/A
    Standard format Plasmid sent in bacteria as agar stab
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    Image Search Results


    16S rDNA similarities, digital DNA–DNA hybridization, and proportions of shared protein-coding genes (⩾70% protein similarity) of the two strains and different members of Methylophilaceae

    Journal: The ISME Journal

    Article Title: The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign

    doi: 10.1038/ismej.2015.55

    Figure Lengend Snippet: 16S rDNA similarities, digital DNA–DNA hybridization, and proportions of shared protein-coding genes (⩾70% protein similarity) of the two strains and different members of Methylophilaceae

    Article Snippet: Methylophilus methylotrophus ATCC 53528 , 93.7 , 93.8 , 21.3 , 19.9 , 8.4 , 14.2.

    Techniques: DNA-DNA Hybridization

    (a) Schematic of experimental design to infect K562 cells with FoxA1- or Hnf4a-lentivirus and then perform functional assays on dox-induced cells. In CUT&Tag, a protein A-protein G fusion (pA/G) increases the binding spectrum for Fc-binding and allows Tn5 recruitment to antibody-labeled TF binding sites. In ATAC-seq, Tn5 homes to any accessible site. And in RNA-seq, polyA RNA is captured and sequenced. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1-Hnf4a compared to the number actually activated. Both liver-( P < 10 −38 ) and intestinal-enrichment ( P < 10 −13 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) Genome browser view of a representative liver-specific locus ( ALB ) in FoxA1-Hnf4a clonal line that shows uninduced and induced accessibility, FoxA1 binding, and Hnf4a binding. (d) Meta plot showing uninduced and induced accessibility at all FoxA1-Hnf4a co-bound sites within 50 kb of each FoxA1-Hnf4a activated liver-specific gene (n = 53).

    Journal: bioRxiv

    Article Title: A Test of the Pioneer Factor Hypothesis

    doi: 10.1101/2021.08.17.456650

    Figure Lengend Snippet: (a) Schematic of experimental design to infect K562 cells with FoxA1- or Hnf4a-lentivirus and then perform functional assays on dox-induced cells. In CUT&Tag, a protein A-protein G fusion (pA/G) increases the binding spectrum for Fc-binding and allows Tn5 recruitment to antibody-labeled TF binding sites. In ATAC-seq, Tn5 homes to any accessible site. And in RNA-seq, polyA RNA is captured and sequenced. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1-Hnf4a compared to the number actually activated. Both liver-( P < 10 −38 ) and intestinal-enrichment ( P < 10 −13 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) Genome browser view of a representative liver-specific locus ( ALB ) in FoxA1-Hnf4a clonal line that shows uninduced and induced accessibility, FoxA1 binding, and Hnf4a binding. (d) Meta plot showing uninduced and induced accessibility at all FoxA1-Hnf4a co-bound sites within 50 kb of each FoxA1-Hnf4a activated liver-specific gene (n = 53).

    Article Snippet: We isolated 1e5 cells/sample, and then either used rabbit anti-human FoxA1 monoclonal antibody (Cell Signaling #53528), mouse anti-human Hnf4a monoclonal antibody (Invitrogen #MA1-199), or rabbit anti-human histone H3K4me3 polyclonal antibody (Epicypher #13-0041) as a positive control.

    Techniques: Functional Assay, Binding Assay, Labeling, RNA Sequencing Assay

    (a) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1 compared to the number actually activated. Liver-enrichment ( P < 10 −4 ) is significant. There are 242 total liver-enriched genes. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by Hnf4a compared to the number actually activated. Liver-( P < 10 −8 ) and intestine-enrichment ( P < 10 −15 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) 242 liver genes characterized as activated by Foxa1, Hnf4a, both, or neither. (d) 122 intestine genes characterized as activated by FoxA1, Hnf4a, both, or neither.

    Journal: bioRxiv

    Article Title: A Test of the Pioneer Factor Hypothesis

    doi: 10.1101/2021.08.17.456650

    Figure Lengend Snippet: (a) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by FoxA1 compared to the number actually activated. Liver-enrichment ( P < 10 −4 ) is significant. There are 242 total liver-enriched genes. (b) The number of tissue-specific genes predicted from the hypergeometric distribution to be activated by Hnf4a compared to the number actually activated. Liver-( P < 10 −8 ) and intestine-enrichment ( P < 10 −15 ) are significant. There are 242 total liver-enriched genes and 122 total intestine-enriched genes. (c) 242 liver genes characterized as activated by Foxa1, Hnf4a, both, or neither. (d) 122 intestine genes characterized as activated by FoxA1, Hnf4a, both, or neither.

    Article Snippet: We isolated 1e5 cells/sample, and then either used rabbit anti-human FoxA1 monoclonal antibody (Cell Signaling #53528), mouse anti-human Hnf4a monoclonal antibody (Invitrogen #MA1-199), or rabbit anti-human histone H3K4me3 polyclonal antibody (Epicypher #13-0041) as a positive control.

    Techniques:

    (a) Genome browser view of a representative liver-specific locus ( Arg1 ) in FoxA1 clonal line showing uninduced and induced accessibility and FoxA1 binding. (b) Genome browser view of a representative liver-specific locus ( ApoC3 ) in Hnf4a clonal line showing uninduced and induced accessibility and Hnf4a binding. (c) Meta plot of uninduced and induced accessibility at all FoxA1 binding sites within 50 kb of each FoxA1-activated liver-specific genes (n = 59). (d) Meta plot of uninduced and induced accessibility at all Hnf4a binding sites within 50 kb of each Hnf4a-activated liver-specific genes (n = 76). (e) FoxA1 or Hnf4a motif count at FoxA1 or Hnf4a binding sites within 50 kb of each FoxA1- or Hnf4a-activated liver-specific genes, respectively. Motifs were called with FIMO using 1e-3 a p-value threshold. For each boxplot, the center line represents the median, the box represents the first to third quartiles, and the whiskers represent any points within 1.5 times the interquartile range.

    Journal: bioRxiv

    Article Title: A Test of the Pioneer Factor Hypothesis

    doi: 10.1101/2021.08.17.456650

    Figure Lengend Snippet: (a) Genome browser view of a representative liver-specific locus ( Arg1 ) in FoxA1 clonal line showing uninduced and induced accessibility and FoxA1 binding. (b) Genome browser view of a representative liver-specific locus ( ApoC3 ) in Hnf4a clonal line showing uninduced and induced accessibility and Hnf4a binding. (c) Meta plot of uninduced and induced accessibility at all FoxA1 binding sites within 50 kb of each FoxA1-activated liver-specific genes (n = 59). (d) Meta plot of uninduced and induced accessibility at all Hnf4a binding sites within 50 kb of each Hnf4a-activated liver-specific genes (n = 76). (e) FoxA1 or Hnf4a motif count at FoxA1 or Hnf4a binding sites within 50 kb of each FoxA1- or Hnf4a-activated liver-specific genes, respectively. Motifs were called with FIMO using 1e-3 a p-value threshold. For each boxplot, the center line represents the median, the box represents the first to third quartiles, and the whiskers represent any points within 1.5 times the interquartile range.

    Article Snippet: We isolated 1e5 cells/sample, and then either used rabbit anti-human FoxA1 monoclonal antibody (Cell Signaling #53528), mouse anti-human Hnf4a monoclonal antibody (Invitrogen #MA1-199), or rabbit anti-human histone H3K4me3 polyclonal antibody (Epicypher #13-0041) as a positive control.

    Techniques: Binding Assay

    (a) Venn diagram of all liver genes categorized as either activated by FoxA1, Hnf4a, FoxA1-Hnf4a, some combination, or by none of the three cocktails. (b) Genome browser view of a representative liver-specific locus ( AMDHD1 ) showing examples of a co-bound site that is “FoxA1 Pioneered” (FP), “Hnf4a Pioneered” (HP), and “Collaboratively Co-bound” (CC). The first two tracks are FoxA1 and Hnf4a binding in the FoxA1-Hnf4a co-expression clone and the last two tracks are FoxA1 and Hnf4a binding in their individual expression clones. (c) List of the 31 liver genes that are only activated by FoxA1-Hnf4a co-expression. The columns indicate how many co-bound FP, HP, or CC peaks exist within 100 kb of the gene. (d) Venn diagram of all genome-wide co-bound peaks categorized as either bound by FoxA1 individually (FP), Hnf4a individually (HP), by both, or by neither (CC). (e) Overlap of FP, HP, and CC sites from (D) with ChromHMM annotations showing the fraction of each co-binding site type in each chromatin region.

    Journal: bioRxiv

    Article Title: A Test of the Pioneer Factor Hypothesis

    doi: 10.1101/2021.08.17.456650

    Figure Lengend Snippet: (a) Venn diagram of all liver genes categorized as either activated by FoxA1, Hnf4a, FoxA1-Hnf4a, some combination, or by none of the three cocktails. (b) Genome browser view of a representative liver-specific locus ( AMDHD1 ) showing examples of a co-bound site that is “FoxA1 Pioneered” (FP), “Hnf4a Pioneered” (HP), and “Collaboratively Co-bound” (CC). The first two tracks are FoxA1 and Hnf4a binding in the FoxA1-Hnf4a co-expression clone and the last two tracks are FoxA1 and Hnf4a binding in their individual expression clones. (c) List of the 31 liver genes that are only activated by FoxA1-Hnf4a co-expression. The columns indicate how many co-bound FP, HP, or CC peaks exist within 100 kb of the gene. (d) Venn diagram of all genome-wide co-bound peaks categorized as either bound by FoxA1 individually (FP), Hnf4a individually (HP), by both, or by neither (CC). (e) Overlap of FP, HP, and CC sites from (D) with ChromHMM annotations showing the fraction of each co-binding site type in each chromatin region.

    Article Snippet: We isolated 1e5 cells/sample, and then either used rabbit anti-human FoxA1 monoclonal antibody (Cell Signaling #53528), mouse anti-human Hnf4a monoclonal antibody (Invitrogen #MA1-199), or rabbit anti-human histone H3K4me3 polyclonal antibody (Epicypher #13-0041) as a positive control.

    Techniques: Binding Assay, Expressing, Clone Assay, Genome Wide