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    New England Biolabs monarch rna cleanup kit
    (A) Screening strategy to identify TFs differentially associated between unmethylated and methylated L1HS and L1PA2 copies using curated datasets publicly available in the UniBind database . Note that for each cell line in our panel, we compared each pair of methylated and unmethylated L1 subsets to all ChIP-seq data stored in Unibind (∼3500 datasets), irrespective of the cell-type or conditions in which they were obtained. The rationale was that even if our specific cell line is not necessarily represented in Unibind datasets, a similar cell type may be represented. The main hits were then subsequently confirmed using matched datasets (see panels E and F). (B) Heatmap showing the TF binding enrichment at hypomethylated L1HS and L1PA2 in our panel of cell types. Only the 15 most enriched TFs are shown. (C) Schematic representation of the location of the motifs corresponding to the TFs identified in (B). For TFs binding upstream of L1 insertions, the number of loci with an upstream peak is indicated. (D) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as YY1 and H3K4me3 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in 2102Ep cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (E) DNA methylation level of L1HS bound (+) or unbound (-) by YY1 in embryonal cell lines (H1 and 2102Ep) and other cell lines for which matched YY1 ChIP-seq were also publicly available (K562, HCT116, HepG2, HEK-293T). The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. In H1 cells, the four hypomethylated loci in blue refer to those studied in . (F) DNA methylation levels of L1HS and L1PA2 loci bound (+) or not bound (-) by ESR1, FOXA1, KLF1, KLF5, Myc and EGFR2 in the relevant cell types. ChIP-seq data are matched to the cell line. The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. (G) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as ESR1 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in MCF-7 cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (H) Genome browser view of the BCAS3 locus integrating L1 methylation (bs-ATLAS-seq), expression (poly(A) + <t>RNA-seq),</t> ESR1 binding, as well as H3K4me3 and H3K27ac histone modifications (ChIP-seq). Note the distinctive spliced RNA-seq reads, antisense relative to the L1 element, linking L1 antisense promoter with the adjacent BCAS3 exon. (I) SiRNA-mediated knock-down of ESR1 leads to reduced L1 chimeric transcripts. Top, schematic representation of chimeric transcripts initiated from L1 antisense promoter and leading to truncated or alternative isoforms of the surrounding gene. Upon siRNA-mediated knock down (siESR1), the number of L1 chimeric splice junctions is expected to decrease if ESR1 drives chimeric <t>transcript</t> <t>synthesis,</t> as compared to a scrambled siRNA control (siScr). Bottom left, chimeric transcripts at the BCAS3 locus quantified by the number of normalized spliced-RNA-seq reads (RPM) detected in MCF-7 cells treated by an siRNA against ESR1 (+) or a control scrambled siRNA (-) (data from GSE153250). Bars represent the mean ± s.d. (n=6) and are overlaid by data of individual replicates (one-sided two-sample Wilcoxon test). Bottom right, average chimeric transcripts quantified as the normalized number of splice junctions between L1 and its closest gene in RPM for 42 loci (n=6, mean ± s.d.). The 42 loci are sorted by descending order according to the difference of chimeric transcript levels between cells treated by siESR1 and the control siScr. For 37 loci out of 42 (88%), L1 chimeric transcription is reduced upon ESR1 knock down. The difference is statistically significant for 5 loci (one-sided two-sample Wilcoxon test). In panels (E) and (F), boxplots represent the median and interquartile range (IQR) ± 1.5 * IQR (whiskers). Outliers beyond the end of the whiskers are plotted individually. *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001, two-sided two-sample Wilcoxon test. See also .
    Monarch Rna Cleanup Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Resolving the heterogeneity of L1 DNA methylation reveals the epigenetic and transcriptional interplay between L1s and their integration sites"

    Article Title: Resolving the heterogeneity of L1 DNA methylation reveals the epigenetic and transcriptional interplay between L1s and their integration sites

    Journal: bioRxiv

    doi: 10.1101/2023.01.03.522582

    (A) Screening strategy to identify TFs differentially associated between unmethylated and methylated L1HS and L1PA2 copies using curated datasets publicly available in the UniBind database . Note that for each cell line in our panel, we compared each pair of methylated and unmethylated L1 subsets to all ChIP-seq data stored in Unibind (∼3500 datasets), irrespective of the cell-type or conditions in which they were obtained. The rationale was that even if our specific cell line is not necessarily represented in Unibind datasets, a similar cell type may be represented. The main hits were then subsequently confirmed using matched datasets (see panels E and F). (B) Heatmap showing the TF binding enrichment at hypomethylated L1HS and L1PA2 in our panel of cell types. Only the 15 most enriched TFs are shown. (C) Schematic representation of the location of the motifs corresponding to the TFs identified in (B). For TFs binding upstream of L1 insertions, the number of loci with an upstream peak is indicated. (D) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as YY1 and H3K4me3 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in 2102Ep cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (E) DNA methylation level of L1HS bound (+) or unbound (-) by YY1 in embryonal cell lines (H1 and 2102Ep) and other cell lines for which matched YY1 ChIP-seq were also publicly available (K562, HCT116, HepG2, HEK-293T). The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. In H1 cells, the four hypomethylated loci in blue refer to those studied in . (F) DNA methylation levels of L1HS and L1PA2 loci bound (+) or not bound (-) by ESR1, FOXA1, KLF1, KLF5, Myc and EGFR2 in the relevant cell types. ChIP-seq data are matched to the cell line. The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. (G) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as ESR1 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in MCF-7 cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (H) Genome browser view of the BCAS3 locus integrating L1 methylation (bs-ATLAS-seq), expression (poly(A) + RNA-seq), ESR1 binding, as well as H3K4me3 and H3K27ac histone modifications (ChIP-seq). Note the distinctive spliced RNA-seq reads, antisense relative to the L1 element, linking L1 antisense promoter with the adjacent BCAS3 exon. (I) SiRNA-mediated knock-down of ESR1 leads to reduced L1 chimeric transcripts. Top, schematic representation of chimeric transcripts initiated from L1 antisense promoter and leading to truncated or alternative isoforms of the surrounding gene. Upon siRNA-mediated knock down (siESR1), the number of L1 chimeric splice junctions is expected to decrease if ESR1 drives chimeric transcript synthesis, as compared to a scrambled siRNA control (siScr). Bottom left, chimeric transcripts at the BCAS3 locus quantified by the number of normalized spliced-RNA-seq reads (RPM) detected in MCF-7 cells treated by an siRNA against ESR1 (+) or a control scrambled siRNA (-) (data from GSE153250). Bars represent the mean ± s.d. (n=6) and are overlaid by data of individual replicates (one-sided two-sample Wilcoxon test). Bottom right, average chimeric transcripts quantified as the normalized number of splice junctions between L1 and its closest gene in RPM for 42 loci (n=6, mean ± s.d.). The 42 loci are sorted by descending order according to the difference of chimeric transcript levels between cells treated by siESR1 and the control siScr. For 37 loci out of 42 (88%), L1 chimeric transcription is reduced upon ESR1 knock down. The difference is statistically significant for 5 loci (one-sided two-sample Wilcoxon test). In panels (E) and (F), boxplots represent the median and interquartile range (IQR) ± 1.5 * IQR (whiskers). Outliers beyond the end of the whiskers are plotted individually. *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001, two-sided two-sample Wilcoxon test. See also .
    Figure Legend Snippet: (A) Screening strategy to identify TFs differentially associated between unmethylated and methylated L1HS and L1PA2 copies using curated datasets publicly available in the UniBind database . Note that for each cell line in our panel, we compared each pair of methylated and unmethylated L1 subsets to all ChIP-seq data stored in Unibind (∼3500 datasets), irrespective of the cell-type or conditions in which they were obtained. The rationale was that even if our specific cell line is not necessarily represented in Unibind datasets, a similar cell type may be represented. The main hits were then subsequently confirmed using matched datasets (see panels E and F). (B) Heatmap showing the TF binding enrichment at hypomethylated L1HS and L1PA2 in our panel of cell types. Only the 15 most enriched TFs are shown. (C) Schematic representation of the location of the motifs corresponding to the TFs identified in (B). For TFs binding upstream of L1 insertions, the number of loci with an upstream peak is indicated. (D) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as YY1 and H3K4me3 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in 2102Ep cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (E) DNA methylation level of L1HS bound (+) or unbound (-) by YY1 in embryonal cell lines (H1 and 2102Ep) and other cell lines for which matched YY1 ChIP-seq were also publicly available (K562, HCT116, HepG2, HEK-293T). The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. In H1 cells, the four hypomethylated loci in blue refer to those studied in . (F) DNA methylation levels of L1HS and L1PA2 loci bound (+) or not bound (-) by ESR1, FOXA1, KLF1, KLF5, Myc and EGFR2 in the relevant cell types. ChIP-seq data are matched to the cell line. The number of L1HS copies in each subset (n) is indicated at the bottom of the plot. (G) Heatmap displaying L1 methylation (bs-ATLAS-seq), as well as ESR1 binding (ChIP-seq), at the 5’ junction (−1 to +0.5 kb) of L1HS and L1PA2 elements in MCF-7 cells. Loci are sorted by increasing levels of L1 methylation. ChIP-seq signal represents the number of normalized reads per 10-bp bin. (H) Genome browser view of the BCAS3 locus integrating L1 methylation (bs-ATLAS-seq), expression (poly(A) + RNA-seq), ESR1 binding, as well as H3K4me3 and H3K27ac histone modifications (ChIP-seq). Note the distinctive spliced RNA-seq reads, antisense relative to the L1 element, linking L1 antisense promoter with the adjacent BCAS3 exon. (I) SiRNA-mediated knock-down of ESR1 leads to reduced L1 chimeric transcripts. Top, schematic representation of chimeric transcripts initiated from L1 antisense promoter and leading to truncated or alternative isoforms of the surrounding gene. Upon siRNA-mediated knock down (siESR1), the number of L1 chimeric splice junctions is expected to decrease if ESR1 drives chimeric transcript synthesis, as compared to a scrambled siRNA control (siScr). Bottom left, chimeric transcripts at the BCAS3 locus quantified by the number of normalized spliced-RNA-seq reads (RPM) detected in MCF-7 cells treated by an siRNA against ESR1 (+) or a control scrambled siRNA (-) (data from GSE153250). Bars represent the mean ± s.d. (n=6) and are overlaid by data of individual replicates (one-sided two-sample Wilcoxon test). Bottom right, average chimeric transcripts quantified as the normalized number of splice junctions between L1 and its closest gene in RPM for 42 loci (n=6, mean ± s.d.). The 42 loci are sorted by descending order according to the difference of chimeric transcript levels between cells treated by siESR1 and the control siScr. For 37 loci out of 42 (88%), L1 chimeric transcription is reduced upon ESR1 knock down. The difference is statistically significant for 5 loci (one-sided two-sample Wilcoxon test). In panels (E) and (F), boxplots represent the median and interquartile range (IQR) ± 1.5 * IQR (whiskers). Outliers beyond the end of the whiskers are plotted individually. *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001, two-sided two-sample Wilcoxon test. See also .

    Techniques Used: Methylation, ChIP-sequencing, Binding Assay, DNA Methylation Assay, Expressing, RNA Sequencing Assay

    monarch rna cleanup kit  (New England Biolabs)


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    New England Biolabs monarch rna cleanup kit
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    monarch rna cleanup kit  (New England Biolabs)


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    New England Biolabs monarch rna cleanup kit

    Monarch Rna Cleanup Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/monarch rna cleanup kit/product/New England Biolabs
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    1) Product Images from "Hypoxia induces transgenerational epigenetic inheritance of small RNAs"

    Article Title: Hypoxia induces transgenerational epigenetic inheritance of small RNAs

    Journal: Cell reports

    doi: 10.1016/j.celrep.2022.111800


    Figure Legend Snippet:

    Techniques Used: Recombinant, Western Blot, Bradford Assay, Isolation, Sequencing, Mutagenesis, Northern Blot, Plasmid Preparation, Software, Microscopy, Imaging, Magnetic Beads

    monarch rna cleanup kit  (New England Biolabs)


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    New England Biolabs monarch rna cleanup kit

    Monarch Rna Cleanup Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/monarch rna cleanup kit/product/New England Biolabs
    Average 86 stars, based on 1 article reviews
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    1) Product Images from "Hypoxia induces transgenerational epigenetic inheritance of small RNAs"

    Article Title: Hypoxia induces transgenerational epigenetic inheritance of small RNAs

    Journal: Cell reports

    doi: 10.1016/j.celrep.2022.111800


    Figure Legend Snippet:

    Techniques Used: Recombinant, Western Blot, Bradford Assay, Isolation, Sequencing, Mutagenesis, Northern Blot, Plasmid Preparation, Software, Microscopy, Imaging, Magnetic Beads

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