m 280 streptavidin coated dynabeads  (Thermo Fisher)


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    Structured Review

    Thermo Fisher m 280 streptavidin coated dynabeads
    Components and performance of the INTACT system ( A ) Confocal projection of the differentiation zone of an ADF8p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in hair cells. GFP signal is shown in green and propidium iodide staining of cell walls is shown in red. ( B ) Confocal projection of the differentiation zone of an GL2p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in non-hair cells. ( C ) Confocal section of the post-meristematic region of a GL2p : NTF/ACT2p : BirA transgenic root. ( D ) Fluorescence micrograph of nuclei (one is shown in inset) isolated from ADF8p : NTF/ACT2p : BirA transgenic roots and incubated with <t>streptavidin</t> <t>Dynabeads.</t> GFP and beads are shown in green and DAPI staining of DNA is shown in blue. ( E ) Streptavidin western blot of whole cell extracts (input) and anti-GFP immunoprecipitates (IP) from roots of ACT2p : BirA, ADF8p : NTF/ACT2p : BirA , and GL2p : NTF/ACT2p : BirA plants. Top and bottom bands in each lane are endogenous biotinylated proteins and the middle band is the 42 kD NTF. ( F ) Diagram of the apparatus used for purification of biotinylated nuclei. See also .
    M 280 Streptavidin Coated Dynabeads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    m 280 streptavidin coated dynabeads - by Bioz Stars, 2020-01
    99/100 stars

    Images

    1) Product Images from "A simple method for gene expression and chromatin profiling of individual cell types within a tissue"

    Article Title: A simple method for gene expression and chromatin profiling of individual cell types within a tissue

    Journal:

    doi: 10.1016/j.devcel.2010.05.013

    Components and performance of the INTACT system ( A ) Confocal projection of the differentiation zone of an ADF8p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in hair cells. GFP signal is shown in green and propidium iodide staining of cell walls is shown in red. ( B ) Confocal projection of the differentiation zone of an GL2p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in non-hair cells. ( C ) Confocal section of the post-meristematic region of a GL2p : NTF/ACT2p : BirA transgenic root. ( D ) Fluorescence micrograph of nuclei (one is shown in inset) isolated from ADF8p : NTF/ACT2p : BirA transgenic roots and incubated with streptavidin Dynabeads. GFP and beads are shown in green and DAPI staining of DNA is shown in blue. ( E ) Streptavidin western blot of whole cell extracts (input) and anti-GFP immunoprecipitates (IP) from roots of ACT2p : BirA, ADF8p : NTF/ACT2p : BirA , and GL2p : NTF/ACT2p : BirA plants. Top and bottom bands in each lane are endogenous biotinylated proteins and the middle band is the 42 kD NTF. ( F ) Diagram of the apparatus used for purification of biotinylated nuclei. See also .
    Figure Legend Snippet: Components and performance of the INTACT system ( A ) Confocal projection of the differentiation zone of an ADF8p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in hair cells. GFP signal is shown in green and propidium iodide staining of cell walls is shown in red. ( B ) Confocal projection of the differentiation zone of an GL2p : NTF/ACT2p : BirA transgenic root showing expression of the NTF in non-hair cells. ( C ) Confocal section of the post-meristematic region of a GL2p : NTF/ACT2p : BirA transgenic root. ( D ) Fluorescence micrograph of nuclei (one is shown in inset) isolated from ADF8p : NTF/ACT2p : BirA transgenic roots and incubated with streptavidin Dynabeads. GFP and beads are shown in green and DAPI staining of DNA is shown in blue. ( E ) Streptavidin western blot of whole cell extracts (input) and anti-GFP immunoprecipitates (IP) from roots of ACT2p : BirA, ADF8p : NTF/ACT2p : BirA , and GL2p : NTF/ACT2p : BirA plants. Top and bottom bands in each lane are endogenous biotinylated proteins and the middle band is the 42 kD NTF. ( F ) Diagram of the apparatus used for purification of biotinylated nuclei. See also .

    Techniques Used: Transgenic Assay, Expressing, Staining, Fluorescence, Isolation, Incubation, Western Blot, Purification

    Related Articles

    Centrifugation:

    Article Title: Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation
    Article Snippet: The supernatant was saved after centrifugation and pre-cleared with M-280 Streptavidin Dynabeads (Life Technologies). .. M-280 streptavidin magnetic Dynabeads (Invitrogen) were added to the mixture and incubated for another 30 min at 37 °C with rotation.

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: The lysates were clarified by centrifugation at 14000 × g at 4 °C for 20 min and used directly in pull-down experiments. .. Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol.

    Amplification:

    Article Title: High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing
    Article Snippet: Paragraph title: Amplification and quality control of captured cDNA ... Following hybridisation, human and house pools were washed to eliminate nonspecific hybridization using m-280 streptavidin Dynabeads (Invitrogen 11205D) following recommendations of Roche protocol.

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm.

    Quantitative RT-PCR:

    Article Title: Long Non-coding RNA CDKN2B Antisense RNA 1 Gene Contributes to Paclitaxel Resistance in Endometrial Carcinoma
    Article Snippet: Probes were dissolved in the buffer and incubated with Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 25°C to form probe-coated beads. .. Those probe-coated beads were incubated with the lysates from Ishikawa/PA and HEC1A/PA cells, and eluted with the washing buffer.

    Article Title: Long Non-coding RNA TUSC7, a Target of miR-23b, Plays Tumor-Suppressing Roles in Human Gliomas
    Article Snippet: The samples were incubated with Dynabeads M-280 Streptavidin (Invitrogen, Carlsbad, CA, USA). .. Biotinylated miR-23b was incubated with beads for 10 min, and treated with washing buffer.

    Article Title: LINC00702 suppresses proliferation and invasion in non-small cell lung cancer through regulating miR-510/PTEN axis
    Article Snippet: Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, USA) was used for pull-down assay according to the manufacturer’s protocol. .. Briefly, the washed beads were incubated with equal volume of biotinylated negative control, miR-510 or miR-510 MT at 25°C in binding and washing buffer for 10 min. Later on, the immobilized miR-510 fragment enriched in the beads were incubated with 10 mM EDTA (pH = 8.2) with 95% formamide at 60°C for 10 min.

    Microarray:

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: The robot is capable of handling 48 samples in parallel, which is the same number as can be hybridized to one microarray slide. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product.

    Incubation:

    Article Title: Long Non-coding RNA CDKN2B Antisense RNA 1 Gene Contributes to Paclitaxel Resistance in Endometrial Carcinoma
    Article Snippet: The biotinylated probes for CDKN2B-AS and miR-125a-5p (bio-CDKN2B-AS-W and bio-miR-125a-5p-W, containing wild-type binding site), as well as their negative controls (bio-CDKN2B-AS-M and bio-miR-125a-5p-M, containing mutant binding site) were synthetized by GenePharma Co. Ltd. (Shanghai, China). .. Probes were dissolved in the buffer and incubated with Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 25°C to form probe-coated beads. .. Those probe-coated beads were incubated with the lysates from Ishikawa/PA and HEC1A/PA cells, and eluted with the washing buffer.

    Article Title: Long Non-coding RNA TUSC7, a Target of miR-23b, Plays Tumor-Suppressing Roles in Human Gliomas
    Article Snippet: Probes for miR-23b or TUSC7 were biotinylated (Sangon, Shanghai, China) and transfected into glioma cells. .. The samples were incubated with Dynabeads M-280 Streptavidin (Invitrogen, Carlsbad, CA, USA). .. Biotinylated miR-23b was incubated with beads for 10 min, and treated with washing buffer.

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: For primer sequences see . .. 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. Beads were washed for three times with TEN buffer and blocked by incubating with 5 mg/ml BSA in TEN buffer for 1 h at 4°C while rotating.

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Wt‐MALAT1 and mut‐MALAT1 as well as wt‐HDAC4 and mut‐HDAC4 were transcribed from vector pGEM® ‐T (Promega) and biotin‐labeled with the Biotin RNA Labeling Mix (Roche, Basel, Switzerland) and T7 RNA polymerase (Roche), treated with RNase‐free DNase I (Roche), and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). .. The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol. .. Then, HOS and 143B cell lysates were incubated with the probe‐coated beads, and the RNA complexes bound to these beads were eluted and extracted for qRT‐PCR analysis to detect the relative expression of miR‐140‐5p.

    Article Title: Reverse Engineering of Vaccine Antigens Using High Throughput Sequencing-enhanced mRNA Display
    Article Snippet: Experimenters who performed the neutralization assay were blinded. .. 2.9 A total of 20 μg of biotinylated synthetic peptides were incubated with 100 μl of Dynabeads M-280 Streptavidin (Life Technologies) at room temperature for 1 h. After washing with PBS (pH 7.4), the beads were blocked with 5% milk in phosphate-buffered saline (PBS), and incubated with diluted polyclonal serum at room temperature for 1 h. The beads were pelleted with a magnet stand, and the supernatant was collected for further analysis. .. 2.10 Statistical analysis was performed with GraphPad Prism 6 using an unpaired Student t test with a two-tailed p value.

    Article Title: Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome
    Article Snippet: Pellets were resuspended in 20 μl H2 O, incubated at 65°C for 2 min, snap-cooled on ice, and incubated for 30 min on ice with 5 μl 1 N NaOH. .. During the hydrolysis step, 300 μl (3 × 50 μl per library) Dynabeads M-280 Streptavidin beads (Invitrogen 11206D) were washed twice with 1 ml M-280 high salt wash (50 mM Tris pH 7.8, 2 M NaCl, 0.5% Triton X-100, and 1 mM EDTA) and resuspended with 300 μl M-280 high salt wash. Dynabeads were stored at 4°C with rotation until needed (no more than a few days).

    Article Title: Dynamic m6A mRNA methylation directs translational control of heat shock response
    Article Snippet: The final products in formaldehyde gels were isolated by Zymoclean™ Gel RNA Recovery Kit (Zymo Research). .. To isolate endogenous Hsp70 mRNA, 400 pmol of biotin-labeled probe (5′-TTCATAACATATCTCTGTCTCTT-3′) was incubated with of 2 mg M-280 Streptavidin Dynabeads (Life Technologies) in 1 ml 1× B & W buffer (5 mM Tris-HCL pH 7.5, 0.5 mM EDTA and 1 M NaCl) at 4°C for 1 hr. .. 2 mg total RNA was denatured at 75°C for 2 min and added to the pre-coated Dynabeads for an additional incubation of 2 h at 4°C.

    Article Title: Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation
    Article Snippet: A small amount of pre-cleared samples were saved as input as the remaining was incubated with biotinylated antisense or sense oligos at 4 °C overnight. .. M-280 streptavidin magnetic Dynabeads (Invitrogen) were added to the mixture and incubated for another 30 min at 37 °C with rotation. .. Beads were captured by magnets (Life Technologies) and washed five times with buffer (300 mM Nacl, 30 mM sodium citrate, 0.5% SDS, PMSF, Roche cocktail proteinase inhibitor, SUPERaseIn RNase inhibitor).

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol. .. Briefly, beads were suspended in 350 μL binding buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl) and coated with 100 pmol of siRNA (100 μL) by gently rocking for 30 min at room temperature.

    Expressing:

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: Cells expressing FLAG-Avi–tagged full-length EphB2 without BirA addition were used as unbiotinylated control. .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: For co-precipitation of transiently expressed proteins, 293FT cells were transfected by standard calcium phosphate precipitation method with expression vectors encoding different nsP3 proteins tagged with the biotin acceptor domain together with an equimolar amount of a vector for Myc epitope-tagged amphiphysin-1 (Gen Bank accession BC034376) or amphiphysin-2 (ubiquitous isoform #9; Gen Bank accession BC004101), corresponding to a total of 10–16 µg of plasmid DNA per 10 cm culture dish. .. NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen).

    Western Blot:

    Article Title: MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
    Article Snippet: Paragraph title: Western Blot Analysis, bio-IPs and purification of Detergent Resistant Membrane (DRM) fractions ... The biotinylated protein complex is precipitated using paramagnetic streptavidin beads (Dynabeads M-280, Invitrogen) for 1 hour at 4°C.

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: Paragraph title: Protein pull-downs and Western blots ... NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen).

    Hybridization:

    Article Title: High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing
    Article Snippet: Blockers: Additional blockers targeting the SMARTer adaptors used during library construction (sequences in , “SMARTer_blocker” and “SMARTer_5p_PCR_blocker”). .. Following hybridisation, human and house pools were washed to eliminate nonspecific hybridization using m-280 streptavidin Dynabeads (Invitrogen 11205D) following recommendations of Roche protocol. .. Human and Mouse washed pools were PCR amplified using KAPA HotStart ReadyMix- 2X (KapaBiosysthems KK1006).

    Article Title: Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing
    Article Snippet: A 7-μl mix containing 2.5 μg human C0 t-1 DNA (Invitrogen), 2.5 μg salmon sperm DNA (Stratagene) and 500 ng whole genome fragment library was heated for 5 min. at 95°, held for 5 min. at 65° in a PCR machine and mixed with 13 μl prewarmed (65°C) 2X hybridization buffer (10X SSPE, 10X Denhardt’s, 10 mM EDTA and 0.2% SDS) and a 6-μl freshly prepared, prewarmed (2 min. at 65°C) mix of 500 ng biotinylated RNA and 20 U SUPERase-In. .. After 66 h at 65°C, the hybridization mix was added to 500 ng (50 μl) M-280 streptavidin Dynabeads (Invitrogen), that had been washed 3 times and were resuspended in 200 μl 1M NaCl, 10 mM Tris-HCl, pH 7.5, and 1 mM EDTA. .. After 30 min. at RT, the beads were pulled down and washed once at RT for 15 min. with 0.5 ml 1X SSC/0.1% SDS, followed by three 10-min. washes at 65°C with 0.5 ml prewarmed 0.1X SSC/0.1% SDS, resupending the beads once at each washing step.

    Transfection:

    Article Title: Long Non-coding RNA TUSC7, a Target of miR-23b, Plays Tumor-Suppressing Roles in Human Gliomas
    Article Snippet: Probes for miR-23b or TUSC7 were biotinylated (Sangon, Shanghai, China) and transfected into glioma cells. .. The samples were incubated with Dynabeads M-280 Streptavidin (Invitrogen, Carlsbad, CA, USA).

    Article Title: LINC00702 suppresses proliferation and invasion in non-small cell lung cancer through regulating miR-510/PTEN axis
    Article Snippet: NCI-H441 and PC-9 cells were transiently transfected with biotinylated negative control, miR-510 or miR-510 MT (Genepharma, China) for 72 h. The cells were harvested after transfection and 50 μL of the samples were aliquoted for input. .. Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, USA) was used for pull-down assay according to the manufacturer’s protocol.

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: To do this, 1.5 µg of plasmid encoding FLAG-Avi–tagged full-length EphB2 or 0.5 µg of plasmid encoding FLAG-Avi-tagged EphB2ΔC was transfected into HeLa cells cultured in 100-mm dishes using Lipofectamine 2000 (Thermo Fisher Scientific). .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: After 24 h of transfection, cells were collected in PBG buffer (1x phosphate buffered saline (PBS) supplemented with 10% glycerol and 0.5% Tween-20) containing protease inhibitors (“Complete”, Roche) and lysed by sonication at 0.2–0.3 kJ on ice by Bandelin Sonoplus homogenizer. .. NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen).

    Chromatography:

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering. .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Ligation:

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH. .. Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH.

    Protease Inhibitor:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. A PCR fragment amplified from a plasmid containing the BRAF1 gene (pLVX-BRAF1 ) was used as a negative control.

    Article Title: MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
    Article Snippet: After washing with PBS, cells were lysed for 30 min on ice in non-denaturing lysis buffer (NDLB: 20 mM Tris-Cl pH 7,6, 110 mM NaCl, 2 mM EDTA, 0,3% NP-40 and 10% glycerol, Supplemented with phosphatase inhibitors (30 mM NaF, 1 mM Na3 VO4 , 2 mM Na2 MoO4 , 5 mM Na4 P2 O7 ) and 1X Complete protease inhibitor cocktail (Roche). .. The biotinylated protein complex is precipitated using paramagnetic streptavidin beads (Dynabeads M-280, Invitrogen) for 1 hour at 4°C.

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: The interferon-treated cells were washed twice with PBS and lysed by shaking with 3 mL solubilization buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, supplemented with protease inhibitor cocktail (ProteoBlock, Fermentas) for 30 min on ice. .. Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol.

    Cell Culture:

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: To do this, 1.5 µg of plasmid encoding FLAG-Avi–tagged full-length EphB2 or 0.5 µg of plasmid encoding FLAG-Avi-tagged EphB2ΔC was transfected into HeLa cells cultured in 100-mm dishes using Lipofectamine 2000 (Thermo Fisher Scientific). .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    other:

    Article Title: Specific Magnetic Isolation of E6 HPV16 Modified Magnetizable Particles Coupled with PCR and Electrochemical Detection
    Article Snippet: 10 mg·mL−1 of commercial Dynabeads M-280 Streptavidin (Invitrogen) in phosphate buffered saline (PBS) pH 7.4 with 0.09% sodium azide as a preservative were used in this study.

    DNA Sequencing:

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D). .. For ChIRP-Seq, DNA was eluted from streptavidin beads by reverse-crosslinking overnight at 65 °C followed by DNA extraction with the QIAGEN DNeasy Blood and Tissue Kit (Cat #69504).

    Protein Concentration:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. Next, S phase-synchronized cells were lysed in lysis buffer [50 mM HEPES–KOH (pH 7.5), 100 mM KCl, 5 mM MgCl2 , 1 mM EDTA, 5% glycerol, 1% Triton X-100, 3 mM DTT and protease inhibitor cocktail].

    Sequencing:

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: LincDUSP-specific tiling biotinylated oligonucleotides were designed from the mature lincDUSP sequence using the Biosearch Technologies ChIRP Probe Designer tool (v 4.1) ( https://www.biosearchtech.com/chirpdesigner/ ). .. ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D).

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: Paragraph title: EmRiboSeq library preparation and sequencing ... Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH.

    Sonication:

    Article Title: Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation
    Article Snippet: Cells were pelleted by centrifugation at 2000 × g for 5 min and lysed in buffer containing 50 mM Tris pH 7.0, 10 mM EDTA, 1% SDS, complete proteinase inhibitor (Roche), and RNase inhibitor (Vazyme) for 20 min on ice, then subjected to sonication for 10 min or until the lysate turns clear. .. M-280 streptavidin magnetic Dynabeads (Invitrogen) were added to the mixture and incubated for another 30 min at 37 °C with rotation.

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: After 24 h of transfection, cells were collected in PBG buffer (1x phosphate buffered saline (PBS) supplemented with 10% glycerol and 0.5% Tween-20) containing protease inhibitors (“Complete”, Roche) and lysed by sonication at 0.2–0.3 kJ on ice by Bandelin Sonoplus homogenizer. .. NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen).

    Affinity Purification:

    Article Title: Selenocysteine tRNA[Ser]Sec, the Central Component of Selenoprotein Biosynthesis: Isolation, Identification, Modification and Sequencing
    Article Snippet: Paragraph title: 2.6 Affinity Purification of tRNA[Ser]Sec ... Streptavidin-conjugated magnetic M-280 Dynabeads (Thermo Fisher Scientific, Waltham, MA).

    Binding Assay:

    Article Title: Long Non-coding RNA CDKN2B Antisense RNA 1 Gene Contributes to Paclitaxel Resistance in Endometrial Carcinoma
    Article Snippet: The biotinylated probes for CDKN2B-AS and miR-125a-5p (bio-CDKN2B-AS-W and bio-miR-125a-5p-W, containing wild-type binding site), as well as their negative controls (bio-CDKN2B-AS-M and bio-miR-125a-5p-M, containing mutant binding site) were synthetized by GenePharma Co. Ltd. (Shanghai, China). .. Probes were dissolved in the buffer and incubated with Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 25°C to form probe-coated beads.

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Wt‐MALAT1 and mut‐MALAT1 as well as wt‐HDAC4 and mut‐HDAC4 were transcribed from vector pGEM® ‐T (Promega) and biotin‐labeled with the Biotin RNA Labeling Mix (Roche, Basel, Switzerland) and T7 RNA polymerase (Roche), treated with RNase‐free DNase I (Roche), and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). .. The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol. .. Then, HOS and 143B cell lysates were incubated with the probe‐coated beads, and the RNA complexes bound to these beads were eluted and extracted for qRT‐PCR analysis to detect the relative expression of miR‐140‐5p.

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: Paragraph title: SiRNA-PKR Binding Assay ... Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol.

    DNA Extraction:

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D). .. ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D).

    Pull Down Assay:

    Article Title: Long Non-coding RNA CDKN2B Antisense RNA 1 Gene Contributes to Paclitaxel Resistance in Endometrial Carcinoma
    Article Snippet: Paragraph title: RNA Pull-Down Assay ... Probes were dissolved in the buffer and incubated with Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 25°C to form probe-coated beads.

    Article Title: Long Non-coding RNA TUSC7, a Target of miR-23b, Plays Tumor-Suppressing Roles in Human Gliomas
    Article Snippet: Paragraph title: RNA Pull-Down Assay ... The samples were incubated with Dynabeads M-280 Streptavidin (Invitrogen, Carlsbad, CA, USA).

    Article Title: LINC00702 suppresses proliferation and invasion in non-small cell lung cancer through regulating miR-510/PTEN axis
    Article Snippet: NCI-H441 and PC-9 cells were transiently transfected with biotinylated negative control, miR-510 or miR-510 MT (Genepharma, China) for 72 h. The cells were harvested after transfection and 50 μL of the samples were aliquoted for input. .. Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, USA) was used for pull-down assay according to the manufacturer’s protocol. .. Briefly, the washed beads were incubated with equal volume of biotinylated negative control, miR-510 or miR-510 MT at 25°C in binding and washing buffer for 10 min. Later on, the immobilized miR-510 fragment enriched in the beads were incubated with 10 mM EDTA (pH = 8.2) with 95% formamide at 60°C for 10 min.

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Paragraph title: RNA pull‐down assay ... The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol.

    Fluorescence:

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product.

    Magnetic Beads:

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: After 24 h of transfection, cells were collected in PBG buffer (1x phosphate buffered saline (PBS) supplemented with 10% glycerol and 0.5% Tween-20) containing protease inhibitors (“Complete”, Roche) and lysed by sonication at 0.2–0.3 kJ on ice by Bandelin Sonoplus homogenizer. .. NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen). .. Whole-cell extracts (WCEs) and precipitated material were analyzed by Western blotting, where mouse anti-Myc antibody together with IRDye-labeled secondary anti-mouse antibody were used for detection of amphiphysins and the IRDye-labeled streptavidin was used for detection of nsP3 proteins by Odyssey infrared imaging system (LI-COR Biosciences).

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: The PrASE assay was automated by the use of a Magnatrix 1200 pipetting robot (Magnetic Biosolutions) that handles magnetic beads used for streptavidin immobilization of the biotinylated PCR products. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product.

    Mutagenesis:

    Article Title: Long Non-coding RNA CDKN2B Antisense RNA 1 Gene Contributes to Paclitaxel Resistance in Endometrial Carcinoma
    Article Snippet: The biotinylated probes for CDKN2B-AS and miR-125a-5p (bio-CDKN2B-AS-W and bio-miR-125a-5p-W, containing wild-type binding site), as well as their negative controls (bio-CDKN2B-AS-M and bio-miR-125a-5p-M, containing mutant binding site) were synthetized by GenePharma Co. Ltd. (Shanghai, China). .. Probes were dissolved in the buffer and incubated with Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 25°C to form probe-coated beads.

    Isolation:

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: Paragraph title: Chromatin Isolation by RNA Purification (ChIRP) ... ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D).

    Article Title: Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome
    Article Snippet: After the CTP pulse, 2.5 μl each of 1 mM biotin-11-ATP (PerkinElmer NEL544), -UTP (NEL543), -GTP (NEL545) and -CTP (NEL542) were added for 10 min. RNA was isolated with Trizol LS, precipitated with 95% ethanol and 500 mM NH4 C2 H3 O2 , and washed with 70% ethanol. .. During the hydrolysis step, 300 μl (3 × 50 μl per library) Dynabeads M-280 Streptavidin beads (Invitrogen 11206D) were washed twice with 1 ml M-280 high salt wash (50 mM Tris pH 7.8, 2 M NaCl, 0.5% Triton X-100, and 1 mM EDTA) and resuspended with 300 μl M-280 high salt wash. Dynabeads were stored at 4°C with rotation until needed (no more than a few days).

    Article Title: Dynamic m6A mRNA methylation directs translational control of heat shock response
    Article Snippet: To isolate endogenous Hsp70 mRNA, 400 pmol of biotin-labeled probe (5′-TTCATAACATATCTCTGTCTCTT-3′) was incubated with of 2 mg M-280 Streptavidin Dynabeads (Life Technologies) in 1 ml 1× B & W buffer (5 mM Tris-HCL pH 7.5, 0.5 mM EDTA and 1 M NaCl) at 4°C for 1 hr. .. 2 mg total RNA was denatured at 75°C for 2 min and added to the pre-coated Dynabeads for an additional incubation of 2 h at 4°C.

    Negative Control:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm.

    Article Title: LINC00702 suppresses proliferation and invasion in non-small cell lung cancer through regulating miR-510/PTEN axis
    Article Snippet: NCI-H441 and PC-9 cells were transiently transfected with biotinylated negative control, miR-510 or miR-510 MT (Genepharma, China) for 72 h. The cells were harvested after transfection and 50 μL of the samples were aliquoted for input. .. Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, USA) was used for pull-down assay according to the manufacturer’s protocol.

    Labeling:

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Wt‐MALAT1 and mut‐MALAT1 as well as wt‐HDAC4 and mut‐HDAC4 were transcribed from vector pGEM® ‐T (Promega) and biotin‐labeled with the Biotin RNA Labeling Mix (Roche, Basel, Switzerland) and T7 RNA polymerase (Roche), treated with RNase‐free DNase I (Roche), and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). .. The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol.

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product.

    Purification:

    Article Title: LINC00702 suppresses proliferation and invasion in non-small cell lung cancer through regulating miR-510/PTEN axis
    Article Snippet: Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, USA) was used for pull-down assay according to the manufacturer’s protocol. .. Briefly, the washed beads were incubated with equal volume of biotinylated negative control, miR-510 or miR-510 MT at 25°C in binding and washing buffer for 10 min. Later on, the immobilized miR-510 fragment enriched in the beads were incubated with 10 mM EDTA (pH = 8.2) with 95% formamide at 60°C for 10 min.

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Wt‐MALAT1 and mut‐MALAT1 as well as wt‐HDAC4 and mut‐HDAC4 were transcribed from vector pGEM® ‐T (Promega) and biotin‐labeled with the Biotin RNA Labeling Mix (Roche, Basel, Switzerland) and T7 RNA polymerase (Roche), treated with RNase‐free DNase I (Roche), and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). .. The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol.

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: Paragraph title: Chromatin Isolation by RNA Purification (ChIRP) ... ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D).

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: Paragraph title: Purification of biotinylated EphB2 interaction proteins ... 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Article Title: Selenocysteine tRNA[Ser]Sec, the Central Component of Selenoprotein Biosynthesis: Isolation, Identification, Modification and Sequencing
    Article Snippet: Purified total tRNA. .. Streptavidin-conjugated magnetic M-280 Dynabeads (Thermo Fisher Scientific, Waltham, MA).

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: After heat inactivation for 15 min at 65°C and Ampure XP purification, DNA was denatured by heating at 95°C for 5 min and snap cooling. .. Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH.

    Article Title: MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
    Article Snippet: Paragraph title: Western Blot Analysis, bio-IPs and purification of Detergent Resistant Membrane (DRM) fractions ... The biotinylated protein complex is precipitated using paramagnetic streptavidin beads (Dynabeads M-280, Invitrogen) for 1 hour at 4°C.

    Polymerase Chain Reaction:

    Article Title: High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing
    Article Snippet: Following hybridisation, human and house pools were washed to eliminate nonspecific hybridization using m-280 streptavidin Dynabeads (Invitrogen 11205D) following recommendations of Roche protocol. .. Human and Mouse washed pools were PCR amplified using KAPA HotStart ReadyMix- 2X (KapaBiosysthems KK1006).

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm.

    Article Title: Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing
    Article Snippet: A 7-μl mix containing 2.5 μg human C0 t-1 DNA (Invitrogen), 2.5 μg salmon sperm DNA (Stratagene) and 500 ng whole genome fragment library was heated for 5 min. at 95°, held for 5 min. at 65° in a PCR machine and mixed with 13 μl prewarmed (65°C) 2X hybridization buffer (10X SSPE, 10X Denhardt’s, 10 mM EDTA and 0.2% SDS) and a 6-μl freshly prepared, prewarmed (2 min. at 65°C) mix of 500 ng biotinylated RNA and 20 U SUPERase-In. .. After 66 h at 65°C, the hybridization mix was added to 500 ng (50 μl) M-280 streptavidin Dynabeads (Invitrogen), that had been washed 3 times and were resuspended in 200 μl 1M NaCl, 10 mM Tris-HCl, pH 7.5, and 1 mM EDTA.

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH. .. Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH.

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: The robot is capable of handling 48 samples in parallel, which is the same number as can be hybridized to one microarray slide. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product. .. Single-stranded DNA was prepared by alkali treatment and annealed to allele-specific extension primers (0.08 μM in 60 μl) (Table S2 from ).

    Immunoprecipitation:

    Article Title: Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
    Article Snippet: Probes were ordered from IDT using 5′-Biotin-TEG and phosphorothioate bond modifications; sequences are shown in Supplementary Table . .. ChIRP was performed for V703 cells as previously described using 500 pmol non-targeting or lincDUSP-specific probes/25 million cells; probes were immunoprecipitated using Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific, Cat #11205D). .. 50 uL beads were removed from each sample for RNA elution to confirm lincDUSP enrichment in lincDUSP pulldown.

    Bradford Protein Assay:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. Next, S phase-synchronized cells were lysed in lysis buffer [50 mM HEPES–KOH (pH 7.5), 100 mM KCl, 5 mM MgCl2 , 1 mM EDTA, 5% glycerol, 1% Triton X-100, 3 mM DTT and protease inhibitor cocktail].

    SDS Page:

    Article Title: MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
    Article Snippet: Postnuclear cell lysates were boiled with reducing SDS sample buffer and analysed by SDS-PAGE on 15% gels. .. The biotinylated protein complex is precipitated using paramagnetic streptavidin beads (Dynabeads M-280, Invitrogen) for 1 hour at 4°C.

    Plasmid Preparation:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: To immobilize the tDNA template, biotinylated primers were used to amplify the tL(CAA)C gene from the plasmid pBS-SK-tRNALEU3 ( ). .. 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm.

    Article Title: Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells. Long noncoding RNA MALAT1 regulates HDAC4‐mediated proliferation and apoptosis via decoying of miR‐140‐5p in osteosarcoma cells
    Article Snippet: Wt‐MALAT1 and mut‐MALAT1 as well as wt‐HDAC4 and mut‐HDAC4 were transcribed from vector pGEM® ‐T (Promega) and biotin‐labeled with the Biotin RNA Labeling Mix (Roche, Basel, Switzerland) and T7 RNA polymerase (Roche), treated with RNase‐free DNase I (Roche), and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). .. The biotinylated MALAT1 and HDAC4 probes were dissolved in binding and washing buffer, and incubated with Dynabeads M‐280 Streptavidin (Invitrogen) at 25°C for 10 minutes to generate probe‐coated beads according to the manufacturer's protocol.

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: To do this, 1.5 µg of plasmid encoding FLAG-Avi–tagged full-length EphB2 or 0.5 µg of plasmid encoding FLAG-Avi-tagged EphB2ΔC was transfected into HeLa cells cultured in 100-mm dishes using Lipofectamine 2000 (Thermo Fisher Scientific). .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Article Title: SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication
    Article Snippet: For co-precipitation of transiently expressed proteins, 293FT cells were transfected by standard calcium phosphate precipitation method with expression vectors encoding different nsP3 proteins tagged with the biotin acceptor domain together with an equimolar amount of a vector for Myc epitope-tagged amphiphysin-1 (Gen Bank accession BC034376) or amphiphysin-2 (ubiquitous isoform #9; Gen Bank accession BC004101), corresponding to a total of 10–16 µg of plasmid DNA per 10 cm culture dish. .. NsP3/amphiphysin complexes were precipitated using streptavidin-coated magnetic beads (Dynabeads M-280-Streptavidin, Invitrogen).

    Multiplex Assay:

    Article Title: Comparison of PrASE and Pyrosequencing for SNP Genotyping
    Article Snippet: The robot is capable of handling 48 samples in parallel, which is the same number as can be hybridized to one microarray slide. .. 200 μg streptavidin-coated super paramagnetic beads (Dynabeads M-280, Dynal Biotech) were used for each inner multiplex PCR product. .. Single-stranded DNA was prepared by alkali treatment and annealed to allele-specific extension primers (0.08 μM in 60 μl) (Table S2 from ).

    Selection:

    Article Title: Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing
    Article Snippet: Paragraph title: Hybrid selection ... After 66 h at 65°C, the hybridization mix was added to 500 ng (50 μl) M-280 streptavidin Dynabeads (Invitrogen), that had been washed 3 times and were resuspended in 200 μl 1M NaCl, 10 mM Tris-HCl, pH 7.5, and 1 mM EDTA.

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH. .. Phusion Flash High-Fidelity PCR Master Mix (Thermo Scientific) was then used for second strand synthesis with primer A to produce a double stranded library.

    In Vitro:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: Paragraph title: In vitro tDNA pull-down experiments ... 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm.

    Article Title: Dynamic m6A mRNA methylation directs translational control of heat shock response
    Article Snippet: To isolate endogenous Hsp70 mRNA, 400 pmol of biotin-labeled probe (5′-TTCATAACATATCTCTGTCTCTT-3′) was incubated with of 2 mg M-280 Streptavidin Dynabeads (Life Technologies) in 1 ml 1× B & W buffer (5 mM Tris-HCL pH 7.5, 0.5 mM EDTA and 1 M NaCl) at 4°C for 1 hr. .. Isolated RNA was quantified using NanoDrop ND-1000 UV-Vis Spectrophotometer and equal amounts of RNAs were mixed with 2× RNA Loading Dye (Thermo Scientific) and denatured for 3 min at 70°C.

    Next-Generation Sequencing:

    Article Title: Lagging strand replication shapes the mutational landscape of the genome
    Article Snippet: Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH. .. Size selection of fragments between 200 and 300 bp in size was performed using 2% E-Gel EX (Life Technologies).

    Spectrophotometry:

    Article Title: Dynamic m6A mRNA methylation directs translational control of heat shock response
    Article Snippet: To isolate endogenous Hsp70 mRNA, 400 pmol of biotin-labeled probe (5′-TTCATAACATATCTCTGTCTCTT-3′) was incubated with of 2 mg M-280 Streptavidin Dynabeads (Life Technologies) in 1 ml 1× B & W buffer (5 mM Tris-HCL pH 7.5, 0.5 mM EDTA and 1 M NaCl) at 4°C for 1 hr. .. Captured RNA was eluted by heating beads for 2 min at 90°C in 10mM EDTA with 95% formamide followed by Trizol LS isolation.

    Concentration Assay:

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: U87 cells (approximately 8 × 106 in a 75 cm2 flask) were treated 24 h before lysis with human interferon-α A (PBL Interferon Source) to a final concentration of 1 × 106 U L−1 . .. Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol.

    Lysis:

    Article Title: Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity
    Article Snippet: 10 μg of biotinylated tDNA was incubated with 1 mg Dynabeads M-280 Streptavidin (Invitrogen) in TEN buffer (5 mM Tris–Cl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl) at 24°C for 24 h with mixing at 1400 rpm. .. A PCR fragment amplified from a plasmid containing the BRAF1 gene (pLVX-BRAF1 ) was used as a negative control.

    Article Title: Exosomes mediate cell contact–independent ephrin-Eph signaling during axon guidance
    Article Snippet: 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering. .. 30 µl of streptavidin-conjugated Dynabeads (Dynabeads M-280 Streptavidin; Thermo Fisher Scientific) were added per dish to induce EphB2 clustering.

    Article Title: MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
    Article Snippet: After washing with PBS, cells were lysed for 30 min on ice in non-denaturing lysis buffer (NDLB: 20 mM Tris-Cl pH 7,6, 110 mM NaCl, 2 mM EDTA, 0,3% NP-40 and 10% glycerol, Supplemented with phosphatase inhibitors (30 mM NaF, 1 mM Na3 VO4 , 2 mM Na2 MoO4 , 5 mM Na4 P2 O7 ) and 1X Complete protease inhibitor cocktail (Roche). .. The biotinylated protein complex is precipitated using paramagnetic streptavidin beads (Dynabeads M-280, Invitrogen) for 1 hour at 4°C.

    Article Title: Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding
    Article Snippet: U87 cells (approximately 8 × 106 in a 75 cm2 flask) were treated 24 h before lysis with human interferon-α A (PBL Interferon Source) to a final concentration of 1 × 106 U L−1 . .. Magnetic streptavidin beads (0.5 mg, 50 μL) (Dynabeads M-280, Invitrogen) were prepared for RNA manipulation according to the manufacturer’s protocol.

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    Thermo Fisher streptavidin coated magnetic beads
    COUP-TFI Is Expressed in bmMSCs and Binds to the Ins2 Promoter (A) The DNA affinity precipitation assay was carried out with the nuclear extracts and biotinylated PCR products. The protein-DNA complexes were separated with <t>streptavidin-labeled</t> beads. The numbers 1 and 2 indicate nuclear extracts from MIN6 cells and from bmMSCs, respectively. (B and C) Western blotting (B) and semiquantitative PCR analysis (C) for COUP-TFI expression levels in MIN6 cells and bmMSCs. (D) MIN6 cells and bmMSCs were stained for COUP-TFI (left) and insulin (middle). Nuclei were stained with DAPI (right). Scale bars represent 50 μm.
    Streptavidin Coated Magnetic Beads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    COUP-TFI Is Expressed in bmMSCs and Binds to the Ins2 Promoter (A) The DNA affinity precipitation assay was carried out with the nuclear extracts and biotinylated PCR products. The protein-DNA complexes were separated with streptavidin-labeled beads. The numbers 1 and 2 indicate nuclear extracts from MIN6 cells and from bmMSCs, respectively. (B and C) Western blotting (B) and semiquantitative PCR analysis (C) for COUP-TFI expression levels in MIN6 cells and bmMSCs. (D) MIN6 cells and bmMSCs were stained for COUP-TFI (left) and insulin (middle). Nuclei were stained with DAPI (right). Scale bars represent 50 μm.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Repression of COUP-TFI Improves Bone Marrow-Derived Mesenchymal Stem Cell Differentiation into Insulin-Producing Cells

    doi: 10.1016/j.omtn.2017.06.016

    Figure Lengend Snippet: COUP-TFI Is Expressed in bmMSCs and Binds to the Ins2 Promoter (A) The DNA affinity precipitation assay was carried out with the nuclear extracts and biotinylated PCR products. The protein-DNA complexes were separated with streptavidin-labeled beads. The numbers 1 and 2 indicate nuclear extracts from MIN6 cells and from bmMSCs, respectively. (B and C) Western blotting (B) and semiquantitative PCR analysis (C) for COUP-TFI expression levels in MIN6 cells and bmMSCs. (D) MIN6 cells and bmMSCs were stained for COUP-TFI (left) and insulin (middle). Nuclei were stained with DAPI (right). Scale bars represent 50 μm.

    Article Snippet: The nuclear extract (200 μg) was incubated at 4°C for 4 hr with biotinylated PCR products previously coupled to streptavidin-coated magnetic beads (Dynabeads M-280; Thermo Scientific).

    Techniques: Affinity Precipitation, Polymerase Chain Reaction, Labeling, Western Blot, Expressing, Staining

    Aβ22-41 binds to fibrinogen and fragment D. (A-B) Biotin-labeled Aβ42, Aβ1-16, Aβ15-25, and Aβ22-41 were incubated with fibrinogen (FBG) or fragment D (FD), and pulldown assays were carried out using streptavidin-coated

    Journal:

    Article Title: Biochemical and structural analysis of the interaction between β-amyloid and fibrinogen

    doi: 10.1182/blood-2016-03-705228

    Figure Lengend Snippet: Aβ22-41 binds to fibrinogen and fragment D. (A-B) Biotin-labeled Aβ42, Aβ1-16, Aβ15-25, and Aβ22-41 were incubated with fibrinogen (FBG) or fragment D (FD), and pulldown assays were carried out using streptavidin-coated

    Article Snippet: Streptavidin-coated magnetic beads (Dynabeads M-280; Thermo-Fisher) were added for 30 minutes, washed, and eluted with nonreducing 1× lithium dodecyl sulfate sample buffer (Thermo Fisher Scientific).

    Techniques: Labeling, Incubation