rna lysis buffer  (New England Biolabs)


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    New England Biolabs rna lysis buffer
    SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 <t>RNA,</t> Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) <t>DNA-FISH</t> for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p
    Rna Lysis Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs"

    Article Title: SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

    Journal: Cell

    doi: 10.1016/j.cell.2017.05.029

    SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 RNA, Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) DNA-FISH for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p
    Figure Legend Snippet: SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 RNA, Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) DNA-FISH for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p

    Techniques Used: Fluorescence In Situ Hybridization, Expressing, Immunofluorescence, Stable Transfection, Binding Assay

    Structural Characteristics of SAF-A and Identification of Walker and Initiator-Specific Motifs, Related to Figure 3 (A) SAF-A encodes four conserved domains: SAP (SAF-A/B, Acinus and PIAS) ( Aravind and Koonin, 2000 ) which has DNA binding activity ( Göhring et al., 1997 ), SPRY (Spla and Ryanodine receptor) of unknown function ( Ponting et al., 1997 ), AAA+ (ATPases Associated with diverse cellular Activities) ( Erzberger and Berger, 2006 ), and a low complexity RGG (arginine glycine-glycine) RNA-binding domain ( Helbig and Fackelmayer, 2003 , Thandapani et al., 2013 ). Probability of protein disorder across SAF-A calculated using different algorithms. Amino acid number is given on x axis while y axis depicts the levels of protein disorder. (B) Sequence and structure homology between SAF-A AAA+ domain and mammalian PNK (PDB-3ZVL) structure showing predicted α helices, β sheets and putative Walker motifs. Conserved amino acids are labeled in red and similar amino acids are marked in yellow. (C) Left, predicted ribbon diagram of SAF-A, modeled on PDB-3ZVL, showing putative Walker motifs and ISM. Right, cartoon of SAF-A protein showing key domains and ISM.
    Figure Legend Snippet: Structural Characteristics of SAF-A and Identification of Walker and Initiator-Specific Motifs, Related to Figure 3 (A) SAF-A encodes four conserved domains: SAP (SAF-A/B, Acinus and PIAS) ( Aravind and Koonin, 2000 ) which has DNA binding activity ( Göhring et al., 1997 ), SPRY (Spla and Ryanodine receptor) of unknown function ( Ponting et al., 1997 ), AAA+ (ATPases Associated with diverse cellular Activities) ( Erzberger and Berger, 2006 ), and a low complexity RGG (arginine glycine-glycine) RNA-binding domain ( Helbig and Fackelmayer, 2003 , Thandapani et al., 2013 ). Probability of protein disorder across SAF-A calculated using different algorithms. Amino acid number is given on x axis while y axis depicts the levels of protein disorder. (B) Sequence and structure homology between SAF-A AAA+ domain and mammalian PNK (PDB-3ZVL) structure showing predicted α helices, β sheets and putative Walker motifs. Conserved amino acids are labeled in red and similar amino acids are marked in yellow. (C) Left, predicted ribbon diagram of SAF-A, modeled on PDB-3ZVL, showing putative Walker motifs and ISM. Right, cartoon of SAF-A protein showing key domains and ISM.

    Techniques Used: Binding Assay, Activity Assay, RNA Binding Assay, Sequencing, Labeling

    2) Product Images from "Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells"

    Article Title: Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells

    Journal: Nature Communications

    doi: 10.1038/s41467-017-01705-y

    CTCs isolated from prostate cancer patient blood contain intact RNA for RNA sequencing and Droplet Digital PCR after whole blood preservation. a RIN values of CTCs isolated from fresh and cold-stored blood (total 15 blood draws from 8 independent patients). b Scaled heatmap of log2-transformed normalized reads (RPMs) for four prostate cancer patients. For patient #3, data are available from three different draw dates stored for different durations (24, 48, and 72 h; denoted #3.1, #3.2, and #3.3, respectively). Statistical analysis comparing fresh vs. cold-stored blood (6 blood draws) found no significant differences in the mean RPMs for any of the 40 genes depicted in b , except for KRT18 ( p = 0.037, paired t -test). c The mRNA copy number of AR-V7 detected by Droplet Digital PCR (expressed as per mL of blood processed). Box-and-whiskers plots show median, interquartile range, maxima, and minima
    Figure Legend Snippet: CTCs isolated from prostate cancer patient blood contain intact RNA for RNA sequencing and Droplet Digital PCR after whole blood preservation. a RIN values of CTCs isolated from fresh and cold-stored blood (total 15 blood draws from 8 independent patients). b Scaled heatmap of log2-transformed normalized reads (RPMs) for four prostate cancer patients. For patient #3, data are available from three different draw dates stored for different durations (24, 48, and 72 h; denoted #3.1, #3.2, and #3.3, respectively). Statistical analysis comparing fresh vs. cold-stored blood (6 blood draws) found no significant differences in the mean RPMs for any of the 40 genes depicted in b , except for KRT18 ( p = 0.037, paired t -test). c The mRNA copy number of AR-V7 detected by Droplet Digital PCR (expressed as per mL of blood processed). Box-and-whiskers plots show median, interquartile range, maxima, and minima

    Techniques Used: Isolation, RNA Sequencing Assay, Digital PCR, Preserving, Transformation Assay

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    New England Biolabs rna lysis buffer
    SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 <t>RNA,</t> Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) <t>DNA-FISH</t> for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p
    Rna Lysis Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna lysis buffer/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rna lysis buffer - by Bioz Stars, 2022-05
    94/100 stars
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    SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 RNA, Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) DNA-FISH for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p

    Journal: Cell

    Article Title: SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

    doi: 10.1016/j.cell.2017.05.029

    Figure Lengend Snippet: SAF-A Oligomerization Regulates Interphase Chromatin Structure via Chromatin-Associated RNAs but Is Not Required to Maintain C 0 t1 and LINE-1 RNA, Related to Figure 6 (A) Boxplots showing the distribution of distances between probe pairs at 2p25.1 from a FISH chromatin compaction assay in cells before (0 hr, red rectangle, box 1), after SAF-A depletion (siSAF-A, dark orange rectangle, box 2) and after re-expression of siRNA-resistant wild-type SAF-A, Walker A or Walker B mutants in the absence (pale orange rectangles, box 3, 5, 7) or presence (green rectangles, box 4, 6, 8) of α-amanitin (n > 100). Colored bars correspond to time points shown in Figure 6 A. (B) Immunofluorescence for SAF-A in Triton X-100 extracted RPE1 cells treated with RNaseA/T1, counterstained with DAPI. Scale bar, 10μm. (C) DNA-FISH for human chromosome 3 (HSA3, C 0 t1 DNA probe) in a human-hamster hybrid cell line (GM10253A) that stably carries HSA3 in conjunction with RNA-FISH to assay for the binding and distribution of caRNAs (C 0 t1 RNA probe) or LINE-1 ORF2 RNA in control cells (siControl) and cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D. Scale bars, 10 μm. (D) Boxplot showing area occupied by HSA3 territory (C 0 t1 DNA probe) as in panel C in GM10253A control cells (siControl), cells depleted for SAF-A (siSAF-A) and cells treated with the transcription inhibitors α-amanitin or actinomycin D (5 h). P values for a Wilcoxon test (n > 30 nuclei; ∗∗∗∗ p

    Article Snippet: The precipitate was suspended in 70% ethanol overnight and resuspended in 50 μL of combined DNA and RNA lysis buffer (1 × DNaseI digestion buffer (NEB) with 1 mM ZnSO4).

    Techniques: Fluorescence In Situ Hybridization, Expressing, Immunofluorescence, Stable Transfection, Binding Assay

    Structural Characteristics of SAF-A and Identification of Walker and Initiator-Specific Motifs, Related to Figure 3 (A) SAF-A encodes four conserved domains: SAP (SAF-A/B, Acinus and PIAS) ( Aravind and Koonin, 2000 ) which has DNA binding activity ( Göhring et al., 1997 ), SPRY (Spla and Ryanodine receptor) of unknown function ( Ponting et al., 1997 ), AAA+ (ATPases Associated with diverse cellular Activities) ( Erzberger and Berger, 2006 ), and a low complexity RGG (arginine glycine-glycine) RNA-binding domain ( Helbig and Fackelmayer, 2003 , Thandapani et al., 2013 ). Probability of protein disorder across SAF-A calculated using different algorithms. Amino acid number is given on x axis while y axis depicts the levels of protein disorder. (B) Sequence and structure homology between SAF-A AAA+ domain and mammalian PNK (PDB-3ZVL) structure showing predicted α helices, β sheets and putative Walker motifs. Conserved amino acids are labeled in red and similar amino acids are marked in yellow. (C) Left, predicted ribbon diagram of SAF-A, modeled on PDB-3ZVL, showing putative Walker motifs and ISM. Right, cartoon of SAF-A protein showing key domains and ISM.

    Journal: Cell

    Article Title: SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

    doi: 10.1016/j.cell.2017.05.029

    Figure Lengend Snippet: Structural Characteristics of SAF-A and Identification of Walker and Initiator-Specific Motifs, Related to Figure 3 (A) SAF-A encodes four conserved domains: SAP (SAF-A/B, Acinus and PIAS) ( Aravind and Koonin, 2000 ) which has DNA binding activity ( Göhring et al., 1997 ), SPRY (Spla and Ryanodine receptor) of unknown function ( Ponting et al., 1997 ), AAA+ (ATPases Associated with diverse cellular Activities) ( Erzberger and Berger, 2006 ), and a low complexity RGG (arginine glycine-glycine) RNA-binding domain ( Helbig and Fackelmayer, 2003 , Thandapani et al., 2013 ). Probability of protein disorder across SAF-A calculated using different algorithms. Amino acid number is given on x axis while y axis depicts the levels of protein disorder. (B) Sequence and structure homology between SAF-A AAA+ domain and mammalian PNK (PDB-3ZVL) structure showing predicted α helices, β sheets and putative Walker motifs. Conserved amino acids are labeled in red and similar amino acids are marked in yellow. (C) Left, predicted ribbon diagram of SAF-A, modeled on PDB-3ZVL, showing putative Walker motifs and ISM. Right, cartoon of SAF-A protein showing key domains and ISM.

    Article Snippet: The precipitate was suspended in 70% ethanol overnight and resuspended in 50 μL of combined DNA and RNA lysis buffer (1 × DNaseI digestion buffer (NEB) with 1 mM ZnSO4).

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

    CTCs isolated from prostate cancer patient blood contain intact RNA for RNA sequencing and Droplet Digital PCR after whole blood preservation. a RIN values of CTCs isolated from fresh and cold-stored blood (total 15 blood draws from 8 independent patients). b Scaled heatmap of log2-transformed normalized reads (RPMs) for four prostate cancer patients. For patient #3, data are available from three different draw dates stored for different durations (24, 48, and 72 h; denoted #3.1, #3.2, and #3.3, respectively). Statistical analysis comparing fresh vs. cold-stored blood (6 blood draws) found no significant differences in the mean RPMs for any of the 40 genes depicted in b , except for KRT18 ( p = 0.037, paired t -test). c The mRNA copy number of AR-V7 detected by Droplet Digital PCR (expressed as per mL of blood processed). Box-and-whiskers plots show median, interquartile range, maxima, and minima

    Journal: Nature Communications

    Article Title: Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells

    doi: 10.1038/s41467-017-01705-y

    Figure Lengend Snippet: CTCs isolated from prostate cancer patient blood contain intact RNA for RNA sequencing and Droplet Digital PCR after whole blood preservation. a RIN values of CTCs isolated from fresh and cold-stored blood (total 15 blood draws from 8 independent patients). b Scaled heatmap of log2-transformed normalized reads (RPMs) for four prostate cancer patients. For patient #3, data are available from three different draw dates stored for different durations (24, 48, and 72 h; denoted #3.1, #3.2, and #3.3, respectively). Statistical analysis comparing fresh vs. cold-stored blood (6 blood draws) found no significant differences in the mean RPMs for any of the 40 genes depicted in b , except for KRT18 ( p = 0.037, paired t -test). c The mRNA copy number of AR-V7 detected by Droplet Digital PCR (expressed as per mL of blood processed). Box-and-whiskers plots show median, interquartile range, maxima, and minima

    Article Snippet: Picked cells were placed into individual PCR tubes containing 5 µL RNA lysis buffer and flash-frozen in liquid nitrogen . cDNA synthesis was performed using the Superscript VILO cDNA synthesis kit and the T4 Gene 32 Protein (New England Biolabs, Cat#M0300S).

    Techniques: Isolation, RNA Sequencing Assay, Digital PCR, Preserving, Transformation Assay