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    Structured Review

    Millipore streptavidine agarose beads
    Sam68 regulates alternative splicing of Sgce exon 8 in male germ cells. RT–PCR analysis of Sgce exon 8 inclusion in total RNA extracted from Sam68 wild-type or knockout testes at 8, 16 and 30 days post partum (dpp) ( A ) or from isolated wild-type or knockout spermatocytes and spermatids. ( B ) Bands corresponding to mRNAs containing or not, exon 8 are indicated on the right of the panels. ( C and D ) Chromatin immunoprecipitation (ChIP) analysis of Sam68 wild-type and knockout germ cells. Sonicated chromatin (100 µg of DNA/sample) was immunoprecipitated with 2µg of H5, H14 antibodies or control rabbit IgGs and co-precipitated DNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( E ) CLIP analysis of the binding of Sam68 to Sgce pre-mRNA. After UV crosslink, Sam68 wild-type and knockout germ cell extracts were sonicated and treated with DNase and RNase to yield RNA fragments of ∼200 to 250 nt. Wild-type and knockout germ cell extracts were immunoprecipitated with 2 µg of rabbit IgGs or anti-Sam68 antibodies and co-precipitated RNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( F ) Electrophoretic mobility shift assays (EMSAs) of the binding of purified GST-Sam68 1–277 to a labelled Sgce probe containing the sequences encoded at the intron 7/exon 8 boundary. The position of the free probe and the probe complexed with GST-Sam68 1–277 are shown on the left side. Competition with the wild-type (middle panel) or mutated (right panel) cold probes is shown. The scheme above the gels shows the wild-type and mutated sequence used in the EMSAs. The mutated bases that interfere with the Sam68 consensus are shown in violet. ( G ) The western blot analysis of RNA pulldown assay of U2AF65 binding to Sgce exon 8. Biotinylated RNAs encoding the Sgce wild-type and mutated exon 8 sequences (from −32 to +63) were bound to <t>Streptavidine</t> agarose beads and incubated with testicular nuclear extract (100 µg) in the presence of 1 µg of purified GST or GST-Sam68 1–277, as indicated.
    Streptavidine Agarose Beads, supplied by Millipore, used in various techniques. Bioz Stars score: 78/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells"

    Article Title: Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr085

    Sam68 regulates alternative splicing of Sgce exon 8 in male germ cells. RT–PCR analysis of Sgce exon 8 inclusion in total RNA extracted from Sam68 wild-type or knockout testes at 8, 16 and 30 days post partum (dpp) ( A ) or from isolated wild-type or knockout spermatocytes and spermatids. ( B ) Bands corresponding to mRNAs containing or not, exon 8 are indicated on the right of the panels. ( C and D ) Chromatin immunoprecipitation (ChIP) analysis of Sam68 wild-type and knockout germ cells. Sonicated chromatin (100 µg of DNA/sample) was immunoprecipitated with 2µg of H5, H14 antibodies or control rabbit IgGs and co-precipitated DNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( E ) CLIP analysis of the binding of Sam68 to Sgce pre-mRNA. After UV crosslink, Sam68 wild-type and knockout germ cell extracts were sonicated and treated with DNase and RNase to yield RNA fragments of ∼200 to 250 nt. Wild-type and knockout germ cell extracts were immunoprecipitated with 2 µg of rabbit IgGs or anti-Sam68 antibodies and co-precipitated RNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( F ) Electrophoretic mobility shift assays (EMSAs) of the binding of purified GST-Sam68 1–277 to a labelled Sgce probe containing the sequences encoded at the intron 7/exon 8 boundary. The position of the free probe and the probe complexed with GST-Sam68 1–277 are shown on the left side. Competition with the wild-type (middle panel) or mutated (right panel) cold probes is shown. The scheme above the gels shows the wild-type and mutated sequence used in the EMSAs. The mutated bases that interfere with the Sam68 consensus are shown in violet. ( G ) The western blot analysis of RNA pulldown assay of U2AF65 binding to Sgce exon 8. Biotinylated RNAs encoding the Sgce wild-type and mutated exon 8 sequences (from −32 to +63) were bound to Streptavidine agarose beads and incubated with testicular nuclear extract (100 µg) in the presence of 1 µg of purified GST or GST-Sam68 1–277, as indicated.
    Figure Legend Snippet: Sam68 regulates alternative splicing of Sgce exon 8 in male germ cells. RT–PCR analysis of Sgce exon 8 inclusion in total RNA extracted from Sam68 wild-type or knockout testes at 8, 16 and 30 days post partum (dpp) ( A ) or from isolated wild-type or knockout spermatocytes and spermatids. ( B ) Bands corresponding to mRNAs containing or not, exon 8 are indicated on the right of the panels. ( C and D ) Chromatin immunoprecipitation (ChIP) analysis of Sam68 wild-type and knockout germ cells. Sonicated chromatin (100 µg of DNA/sample) was immunoprecipitated with 2µg of H5, H14 antibodies or control rabbit IgGs and co-precipitated DNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( E ) CLIP analysis of the binding of Sam68 to Sgce pre-mRNA. After UV crosslink, Sam68 wild-type and knockout germ cell extracts were sonicated and treated with DNase and RNase to yield RNA fragments of ∼200 to 250 nt. Wild-type and knockout germ cell extracts were immunoprecipitated with 2 µg of rabbit IgGs or anti-Sam68 antibodies and co-precipitated RNA was analysed by real time PCR with primers (black arrows in the scheme) spanning the Sgce transcription unit as indicated. ( F ) Electrophoretic mobility shift assays (EMSAs) of the binding of purified GST-Sam68 1–277 to a labelled Sgce probe containing the sequences encoded at the intron 7/exon 8 boundary. The position of the free probe and the probe complexed with GST-Sam68 1–277 are shown on the left side. Competition with the wild-type (middle panel) or mutated (right panel) cold probes is shown. The scheme above the gels shows the wild-type and mutated sequence used in the EMSAs. The mutated bases that interfere with the Sam68 consensus are shown in violet. ( G ) The western blot analysis of RNA pulldown assay of U2AF65 binding to Sgce exon 8. Biotinylated RNAs encoding the Sgce wild-type and mutated exon 8 sequences (from −32 to +63) were bound to Streptavidine agarose beads and incubated with testicular nuclear extract (100 µg) in the presence of 1 µg of purified GST or GST-Sam68 1–277, as indicated.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Knock-Out, Isolation, Chromatin Immunoprecipitation, Sonication, Immunoprecipitation, Real-time Polymerase Chain Reaction, Cross-linking Immunoprecipitation, Binding Assay, Electrophoretic Mobility Shift Assay, Purification, Sequencing, Western Blot, Incubation

    Related Articles

    Transfection:

    Article Title:
    Article Snippet: HL-60 cells transfected with 5 μg of pcDNA3-FOXO3-TM and with or without 10 μg of pcDNA3-Myc-GILZ were harvested 24 h after transfection. .. Double-stranded 5′-biotinylated IRS oligonucleotides of the IGFBP-1 promoter were coupled to streptavidine-agarose beads (Sigma) and nuclear and cytoplasmic extracts were incubated with the precoated beads.

    Amplification:

    Article Title: Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells
    Article Snippet: Amplified DNA was retro-transcribed using Biotinylated NTP Mix (Roche) and purified. .. The 23 dpp testis nuclear extract (100 µg) were pre-cleared on Streptavidine agarose beads (Sigma-Aldrich) in the presence of 1 µg of purified GST or GST-Sam681–277, 0.01% BSA and yeast tRNA for 90 min at 4°C under rotation and then incubated for 30 min at 30°C with Streptavidine beads pre-adsorbed with 500 ng of biotinylated RNA, 0.01% BSA and yeast tRNA.

    Affinity Chromatography:

    Article Title: Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells
    Article Snippet: Paragraph title: RNA affinity chromatography ... The 23 dpp testis nuclear extract (100 µg) were pre-cleared on Streptavidine agarose beads (Sigma-Aldrich) in the presence of 1 µg of purified GST or GST-Sam681–277, 0.01% BSA and yeast tRNA for 90 min at 4°C under rotation and then incubated for 30 min at 30°C with Streptavidine beads pre-adsorbed with 500 ng of biotinylated RNA, 0.01% BSA and yeast tRNA.

    Purification:

    Article Title: Yeast mitochondrial Gln-tRNAGln is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS
    Article Snippet: .. Purification of m tRNAQ and m tRNAE from 1 mg of unfractionated mitochondrial tRNA, prepared as described above, was performed using 5′-biotinylated specific oligonucleotides 15 and 16, respectively (see Supplemental Table 2), immobilized on streptavidine-agarose beads (Novagen) following the procedure described by . .. The standard aminoacylation mixture (100 μL) containing 100 mM Na-Hepes (pH 7.2), 30 mM KCl, 10 mM ATP, 12 mM MgCl2 , 30 μM L-[14 C]glutamate ([14 C]E) (330 cpm/pmol, Amersham) or 1 μM L-[3 H]glutamate ([3 H]E) (3000 cpm/pmol, Amersham), 0.1mg/mL BSA, 0.15 μM pure m tRNAQ or pure m tRNAE or 10 μM total m tRNA, and 0.01 μM m ERS or c ERS was incubated at 30°C.

    Article Title: Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells
    Article Snippet: .. The 23 dpp testis nuclear extract (100 µg) were pre-cleared on Streptavidine agarose beads (Sigma-Aldrich) in the presence of 1 µg of purified GST or GST-Sam681–277, 0.01% BSA and yeast tRNA for 90 min at 4°C under rotation and then incubated for 30 min at 30°C with Streptavidine beads pre-adsorbed with 500 ng of biotinylated RNA, 0.01% BSA and yeast tRNA. ..

    Incubation:

    Article Title:
    Article Snippet: .. Double-stranded 5′-biotinylated IRS oligonucleotides of the IGFBP-1 promoter were coupled to streptavidine-agarose beads (Sigma) and nuclear and cytoplasmic extracts were incubated with the precoated beads. ..

    Article Title: Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells
    Article Snippet: .. The 23 dpp testis nuclear extract (100 µg) were pre-cleared on Streptavidine agarose beads (Sigma-Aldrich) in the presence of 1 µg of purified GST or GST-Sam681–277, 0.01% BSA and yeast tRNA for 90 min at 4°C under rotation and then incubated for 30 min at 30°C with Streptavidine beads pre-adsorbed with 500 ng of biotinylated RNA, 0.01% BSA and yeast tRNA. ..

    Affinity Precipitation:

    Article Title:
    Article Snippet: Paragraph title: DNA Affinity Precipitation of FOXO3 Proteins ... Double-stranded 5′-biotinylated IRS oligonucleotides of the IGFBP-1 promoter were coupled to streptavidine-agarose beads (Sigma) and nuclear and cytoplasmic extracts were incubated with the precoated beads.

    Western Blot:

    Article Title:
    Article Snippet: Double-stranded 5′-biotinylated IRS oligonucleotides of the IGFBP-1 promoter were coupled to streptavidine-agarose beads (Sigma) and nuclear and cytoplasmic extracts were incubated with the precoated beads. .. Western blots were performed using the anti-FOXO3 antibody.

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    Millipore streptavidin agarose beads
    Proline-rich reading array screen and peptide pulldown. (A) Use of biotinylated eVP40 WT (MRRVILPTAPPEYMEAI[Lys-biotin]) peptide (50 μg) to screen a proline-rich reading array. The GST-WW domain fusion proteins are arrayed in duplicate and at different angles, as indicated in enlarged box C. Box C shows duplicate samples of all four WW domains from WWP1, WWP2, and ITCH as indicated. Additional positive interactions are indicated in the highlighted red boxes and ovals (A to H). The eVP40 mutant peptide (MRRVILPTAAAEAMEAI[Lys-biotin]) did not interact with any GST-WW domain fusion protein (data not shown). (B) Exogenously expressed FLAG-tagged WWP1-WT was pulled down with <t>streptavidin</t> beads bound to either eVP40 WT (WT) or PPXY mutant (mut) peptides and detected by Western blotting using anti-Flag antiserum (top). Expression controls for WWP1 and actin are shown (bottom).
    Streptavidin Agarose Beads, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 293 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Proline-rich reading array screen and peptide pulldown. (A) Use of biotinylated eVP40 WT (MRRVILPTAPPEYMEAI[Lys-biotin]) peptide (50 μg) to screen a proline-rich reading array. The GST-WW domain fusion proteins are arrayed in duplicate and at different angles, as indicated in enlarged box C. Box C shows duplicate samples of all four WW domains from WWP1, WWP2, and ITCH as indicated. Additional positive interactions are indicated in the highlighted red boxes and ovals (A to H). The eVP40 mutant peptide (MRRVILPTAAAEAMEAI[Lys-biotin]) did not interact with any GST-WW domain fusion protein (data not shown). (B) Exogenously expressed FLAG-tagged WWP1-WT was pulled down with streptavidin beads bound to either eVP40 WT (WT) or PPXY mutant (mut) peptides and detected by Western blotting using anti-Flag antiserum (top). Expression controls for WWP1 and actin are shown (bottom).

    Journal: Journal of Virology

    Article Title: Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 To Regulate Egress

    doi: 10.1128/JVI.00812-17

    Figure Lengend Snippet: Proline-rich reading array screen and peptide pulldown. (A) Use of biotinylated eVP40 WT (MRRVILPTAPPEYMEAI[Lys-biotin]) peptide (50 μg) to screen a proline-rich reading array. The GST-WW domain fusion proteins are arrayed in duplicate and at different angles, as indicated in enlarged box C. Box C shows duplicate samples of all four WW domains from WWP1, WWP2, and ITCH as indicated. Additional positive interactions are indicated in the highlighted red boxes and ovals (A to H). The eVP40 mutant peptide (MRRVILPTAAAEAMEAI[Lys-biotin]) did not interact with any GST-WW domain fusion protein (data not shown). (B) Exogenously expressed FLAG-tagged WWP1-WT was pulled down with streptavidin beads bound to either eVP40 WT (WT) or PPXY mutant (mut) peptides and detected by Western blotting using anti-Flag antiserum (top). Expression controls for WWP1 and actin are shown (bottom).

    Article Snippet: Streptavidin agarose beads (Millipore) were prewashed once with 1× mild buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.1% NP-40, 5 mM EDTA, 5 mM EGTA, 15 mM MgCl2 ), and 15 μg of the WT or PPXY mutant eVP40 peptide was incubated with the prewashed streptavidin beads in 500 μl of 1× mild buffer for 1 h at 4°C with rocking.

    Techniques: Mutagenesis, Western Blot, Expressing

    The rate of cell surface expression/appearance/transport of BRI2 is reduced in the absence of N-glycosylation. Wild-type mycBRI2 or mycBRI2/N170A was expressed in HEK293 cells. The newly synthesized proteins were labeled with 35 S in radiolabeling medium for 2 h (pulse) at 16°C and then were incubated in non-radiolabeling medium for 0′, 20′, 40′ and 60′ (chase). ( A ) Cell surface proteins were labeled with biotin and precipitated with streptavidin beads. Precipitated cell surface proteins were eluted from the beads and immunoprecipitated with 9B11 antibody against the myc epitope before electrophoresis and autoradiography. ( B ) Immunoprecipitation of cell extracts with 9B11, electrophoresis and autoradiography were performed to verify the expression levels of BRI2.

    Journal: Glycobiology

    Article Title: Glycosylation of BRI2 on asparagine 170 is involved in its trafficking to the cell surface but not in its processing by furin or ADAM10

    doi: 10.1093/glycob/cwr097

    Figure Lengend Snippet: The rate of cell surface expression/appearance/transport of BRI2 is reduced in the absence of N-glycosylation. Wild-type mycBRI2 or mycBRI2/N170A was expressed in HEK293 cells. The newly synthesized proteins were labeled with 35 S in radiolabeling medium for 2 h (pulse) at 16°C and then were incubated in non-radiolabeling medium for 0′, 20′, 40′ and 60′ (chase). ( A ) Cell surface proteins were labeled with biotin and precipitated with streptavidin beads. Precipitated cell surface proteins were eluted from the beads and immunoprecipitated with 9B11 antibody against the myc epitope before electrophoresis and autoradiography. ( B ) Immunoprecipitation of cell extracts with 9B11, electrophoresis and autoradiography were performed to verify the expression levels of BRI2.

    Article Snippet: The cell extracts were centrifuged at 15,000 × g for 30 min and supernatants were incubated with 50 μL of streptavidin–agarose beads (Millipore) for 1 h at 4°C.

    Techniques: Expressing, Synthesized, Labeling, Radioactivity, Incubation, Immunoprecipitation, Electrophoresis, Autoradiography

    Inhibition of N-glycosylation of BRI2 inhibits its expression at the cell surface. Wild-type mycBRI2 or mycBRI2/N170A was expressed in HEK293 cells. Cell surface proteins were labeled with biotin (lanes 1 and 2) or were not labeled (lanes 3 and 4), as a control for biotinylation specificity. ( A ) Cell extracts were precipitated with streptavidin beads and analyzed with western blot against myc with 9B11 antibody. ( B ) Cell extracts were directly analyzed with western blot as a control for protein expression. The two immunoreactive bands of BRI2 proteins correspond to the furin-cleaved and the non-cleaved wild-type mycBRI2 or mycBRI2/N170A.

    Journal: Glycobiology

    Article Title: Glycosylation of BRI2 on asparagine 170 is involved in its trafficking to the cell surface but not in its processing by furin or ADAM10

    doi: 10.1093/glycob/cwr097

    Figure Lengend Snippet: Inhibition of N-glycosylation of BRI2 inhibits its expression at the cell surface. Wild-type mycBRI2 or mycBRI2/N170A was expressed in HEK293 cells. Cell surface proteins were labeled with biotin (lanes 1 and 2) or were not labeled (lanes 3 and 4), as a control for biotinylation specificity. ( A ) Cell extracts were precipitated with streptavidin beads and analyzed with western blot against myc with 9B11 antibody. ( B ) Cell extracts were directly analyzed with western blot as a control for protein expression. The two immunoreactive bands of BRI2 proteins correspond to the furin-cleaved and the non-cleaved wild-type mycBRI2 or mycBRI2/N170A.

    Article Snippet: The cell extracts were centrifuged at 15,000 × g for 30 min and supernatants were incubated with 50 μL of streptavidin–agarose beads (Millipore) for 1 h at 4°C.

    Techniques: Inhibition, Expressing, Labeling, Western Blot

    A19 phosphorylation. (A) Western blot analysis. BS-C-1 cells were infected with vFS-A11 and vFS-A19 in the presence of 100 μCi/ml 32 P i . After 18 h, the cells were lysed, and the soluble extract was bound to streptavidin-agarose beads. Bound proteins

    Journal: Journal of Virology

    Article Title: Vaccinia Virus A19 Protein Participates in the Transformation of Spherical Immature Particles to Barrel-Shaped Infectious Virions

    doi: 10.1128/JVI.01258-13

    Figure Lengend Snippet: A19 phosphorylation. (A) Western blot analysis. BS-C-1 cells were infected with vFS-A11 and vFS-A19 in the presence of 100 μCi/ml 32 P i . After 18 h, the cells were lysed, and the soluble extract was bound to streptavidin-agarose beads. Bound proteins

    Article Snippet: Soluble extracts obtained by low-speed centrifugation were allowed to bind to streptavidin-agarose beads (Millipore, Billerica, MA) for 3 h at 4°C.

    Techniques: Western Blot, Infection

    Expression and characterization of the A19 protein. (A) Schematic representation of the DNA construct used for generating recombinant vFS-A19. The FLAG- and streptavidin-binding peptide tag fused at the N terminus of the A19 ORF (FS) is indicated. The

    Journal: Journal of Virology

    Article Title: Vaccinia Virus A19 Protein Participates in the Transformation of Spherical Immature Particles to Barrel-Shaped Infectious Virions

    doi: 10.1128/JVI.01258-13

    Figure Lengend Snippet: Expression and characterization of the A19 protein. (A) Schematic representation of the DNA construct used for generating recombinant vFS-A19. The FLAG- and streptavidin-binding peptide tag fused at the N terminus of the A19 ORF (FS) is indicated. The

    Article Snippet: Soluble extracts obtained by low-speed centrifugation were allowed to bind to streptavidin-agarose beads (Millipore, Billerica, MA) for 3 h at 4°C.

    Techniques: Expressing, Construct, Recombinant, Binding Assay

    Analysis of viral PPxY-host WW-domain interactions between BAG3 and LFV-Z by peptide pull-down assays. ( A ) Flow chart of the peptide pull-down assay using LFV-Z peptides and cell lysates expressing BAG3-WT; ( B ) Schematic diagram of BAG3-WT, BAG3-ΔN, and BAG3-ΔC mutants with the various domains highlighted in color and amino acid positions indicated; ( C ) Western blot of peptide pull-down assay using streptavidin agarose beads conjugated with either the LFV-Z WT or LFV-Z PY mutant peptide. BAG3 proteins were detected using anti-c-myc antibody (top blot). Expression controls for BAG3 and actin are shown in the bottom blot. These results are from 1 of 2 independent experiments.

    Journal: Diseases

    Article Title: Host Protein BAG3 is a Negative Regulator of Lassa VLP Egress

    doi: 10.3390/diseases6030064

    Figure Lengend Snippet: Analysis of viral PPxY-host WW-domain interactions between BAG3 and LFV-Z by peptide pull-down assays. ( A ) Flow chart of the peptide pull-down assay using LFV-Z peptides and cell lysates expressing BAG3-WT; ( B ) Schematic diagram of BAG3-WT, BAG3-ΔN, and BAG3-ΔC mutants with the various domains highlighted in color and amino acid positions indicated; ( C ) Western blot of peptide pull-down assay using streptavidin agarose beads conjugated with either the LFV-Z WT or LFV-Z PY mutant peptide. BAG3 proteins were detected using anti-c-myc antibody (top blot). Expression controls for BAG3 and actin are shown in the bottom blot. These results are from 1 of 2 independent experiments.

    Article Snippet: Briefly, extracts from HEK293T cells expressing either BAG3-WT, BAG3-ΔN, or BAG3-ΔC ( B) were incubated with streptavidin agarose beads bound with either the LFV-Z-WT or LFV-Z-mutant peptides.

    Techniques: Flow Cytometry, Pull Down Assay, Expressing, Western Blot, Mutagenesis