highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 atto488 rna labeling kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 atto488 rna labeling kit
    a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm <t>(Atto488)</t> fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.
    Highyield T7 Atto488 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes"

    Article Title: Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes

    Journal: Nature Communications

    doi: 10.1038/s41467-022-34644-4

    a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm (Atto488) fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.
    Figure Legend Snippet: a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm (Atto488) fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.

    Techniques Used: Construct, Recombinant, In Vitro, Microscopy, Fluorescence, Whisker Assay, Protein Concentration, Derivative Assay

    highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 rna synthesis kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 atto488 rna labeling kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 atto488 rna labeling kit
    Highyield T7 Atto488 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 cy3 rna labelling kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 cy3 rna labelling kit
    Ubx binds <t>RNA</t> in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by <t>Cy3-UTP</t> signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " width="250" height="auto" />
    Highyield T7 Cy3 Rna Labelling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II"

    Article Title: The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkab1250

    Ubx binds RNA in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by Cy3-UTP signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " title="... ). Interactions were detected on denaturating gels by Cy3-UTP signal (upper panel), and gels were stained by ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: Ubx binds RNA in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by Cy3-UTP signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also Supplementary Figures S11 and S12 , .

    Techniques Used: In Vivo, In Vitro, Immunoprecipitation, Quantitative RT-PCR, Expressing, RNA Expression, Purification, Staining, Marker, RNA Binding Assay

    highyield t7 biontin11 rna labeling kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 biontin11 rna labeling kit
    Highyield T7 Biontin11 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    highyield t7 af488 rna labeling kit  (Jena Bioscience)


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    Jena Bioscience highyield t7 af488 rna labeling kit
    Highyield T7 Af488 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Jena Bioscience highyield t7 rna synthesis kit
    Highyield T7 Rna Synthesis Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Jena Bioscience highyield t7 atto488 rna labeling kit
    a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm <t>(Atto488)</t> fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.
    Highyield T7 Atto488 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Jena Bioscience highyield t7 cy3 rna labelling kit
    Ubx binds <t>RNA</t> in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by <t>Cy3-UTP</t> signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " width="250" height="auto" />
    Highyield T7 Cy3 Rna Labelling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Jena Bioscience highyield t7 biontin11 rna labeling kit
    Ubx binds <t>RNA</t> in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by <t>Cy3-UTP</t> signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " width="250" height="auto" />
    Highyield T7 Biontin11 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Ubx binds <t>RNA</t> in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by <t>Cy3-UTP</t> signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " width="250" height="auto" />
    Highyield T7 Af488 Rna Labeling Kit, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm (Atto488) fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.

    Journal: Nature Communications

    Article Title: Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes

    doi: 10.1038/s41467-022-34644-4

    Figure Lengend Snippet: a Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules. b Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (slncRNA). All scale bars are 10 µm. c Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. d Top - median 488 nm (Atto488) fluorescence intensity values collected from multiple slncRNA granules (blue) and slncRNA-protein granules (orange). Quenching for the slncRNA granules is empirically estimated at 1x for the PCP-4x and PCP-3x/MCP-3x, 1.34x for the PCP-4x/MCP-4x, 1.37 for the PCP-8x, and 4.2x for PCP-14x/MCP-15x. Note that we assume no quenching for the SRNP granules, except for the case of PCP-14x/MCP-15x. Data presented as median values ± SEM. Bottom—Increase in Atto-488 fluorescence between slncRNA-protein granules and slncRNA only granules, for the different slncRNA molecules. Data in top and bottom panels was collected from: 112 PCP-3x/MCP-3x, 165 PCP-4x, 204 PCP-4x/MCP-4x, 121 PCP-8x, and 89 PCP-14x/MCP-15x, RNA-only granule, and from 91 PCP-3x, 69 PCP-3x/MCP-3x, 30 PCP-4x, 92 PCP-4x/MCP-4x, 85 PCP-8x, and 37 PCP-14x/MCP-15x RNA-protein granules. e Structured illumination super resolution images of (left) PCP-14x\MCP-15x slncRNA-protein granule, and (right) PCP-4x slncRNA-protein granules. Color bar indicates fluorescence intensity. f Structured illumination super resolution images of PCP-14x/MCP-14x slncRNA-only granules. Scale bar is 2 µm. Color bar indicates fluorescence intensity. g Microscopy images for serial dilutions of reaction components taken at T = 1 hr after reaction setup. Highest concentrations show the formation of highly fluorescent filamentous structures, as seen in the top left image. Lower RNA concentrations result in smaller structures, while lower protein concentration result in weaker fluorescence. Scale bar is 10 µm. Due to high dynamic range, the intensities presented are the square root of the raw data images. h Maximal observed intensity values for each reaction condition at time T=0 and T=1 hr. All distributions were derived from 5 separate microscopy images of granule reaction prepared with the listed concentrations. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The value for ‘Whisker’ corresponds to ±1.5 IQR (interquartile rate) and extends to the adjacent value, which is the most extreme data value that is not an outlier. The outliers are plotted individually as plus signs. Source data are provided as a Source data file.

    Article Snippet: The enzyme was then heat-inactivated by incubating the restriction reaction at 65 °C for 20 min. For fluorescently labeled RNA, 1 µg of the restriction product was used as template for in vitro transcription using HighYield T7 Atto488 RNA labeling kit (Jena Bioscience, Jena, Germany, RNT-101-488-S), according to the manufacturer’s instructions.

    Techniques: Construct, Recombinant, In Vitro, Microscopy, Fluorescence, Whisker Assay, Protein Concentration, Derivative Assay

    Ubx binds RNA in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by Cy3-UTP signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also <xref ref-type=Supplementary Figures S11 and S12 , . " width="100%" height="100%">

    Journal: Nucleic Acids Research

    Article Title: The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

    doi: 10.1093/nar/gkab1250

    Figure Lengend Snippet: Ubx binds RNA in vivo and in vitro , partly via its Homeodomain. (A–C) RNA-immunoprecipitation (RIP-RT-qPCR) experiments of Drosophila S2R+ cells expressing GFP control (white), GFP-Ubx WT (blue) and GFP-Ubx N51A (purple) showing an enrichment of targeted exonic regions of Chas ( A ), pAbp ( B ) and Rgk1 ( C ). Values are RNA relative enrichment over GFP calculated as percentage of input. The input represents the total RNA detected in each sample and thus, normalises the enrichment to the total RNA expression level. (E + number) = exon related to JunctionSeq annotation, differentially spliced exons are underlined (purple). n = 3 independent biological duplicates. Bars represent mean ± SEM. The results exhibited a specific enrichment of differentially spliced exonic sequences in Ubx WT fraction compared to GFP and Ubx N51A . ( D–K ) Fluorescent protein-RNA interaction assay followed by UV-crosslinking and RNase digestion, performed in vitro with purified proteins namely his-MBP-GFP as control, his-Ubx (WT and N51A) full-length (FL) ( D–G ) and the HD alone his-MBP-Ubx HD (WT and N51A) ( H–K ). Interactions were detected on denaturating gels by Cy3-UTP signal (upper panel), and gels were stained by Coomassie to reveal the protein content (lower panel). Each probe is indicated relative to the genes and exons. Molecular marker is indicated showing the size of each protein. MBP fused proteins are named his-MBP-X, his-fused proteins are named his-X. (L–O) Graphical view showing the quantification of relative RNA-binding of Ubx HD compared to full-length (FL) MBP fused proteins for Chas exon cassette E5 ( L ), constitutive E3, ( M ), pAbp exon cassette E1 ( N ), constitutive E6 ( O ) normalised to Coomassie staining. n = 3 independent biological replicates. Statistical test by one-way ANOVA (* P < 0.05, ** P < 0.01, *** P < 0.001, ns = non-significant). See also Supplementary Figures S11 and S12 , .

    Article Snippet: For producing internally labelled RNA, in vitro transcription was performed using the HighYield T7 Cy3 RNA Labelling Kit (Jena Bioscience, RNT-101-CY3) in accordance to the instructions of the manufacturer.

    Techniques: In Vivo, In Vitro, Immunoprecipitation, Quantitative RT-PCR, Expressing, RNA Expression, Purification, Staining, Marker, RNA Binding Assay