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  • 86
    Diagenode bioruptor
    Library preparation using the CapSMART method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Phosphorylation to add mono-phosphate to the non-capped 5′ end molecules using T4 Polynucleotide Kinase. D) Ligation of STOP oligos. A total of three kinds of oligonucleotides ( Table 2 : STOP1: iGiCiG, STOP2: iCiGiC, STOPMix: mixture of STOP1 and STOP2) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a <t>Bioruptor</t> and collection of biotinylated 5′ ends using beads. H) Illumina sequencing library preparation.
    Bioruptor, supplied by Diagenode, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioruptor/product/Diagenode
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bioruptor - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    86
    Diagenode diagenode bioruptor
    Quantifying hybrid particles presenting both ER and PM markers . The membrane integrity of MelJuSo cells was compromised by EMBL 8.020mm “cell cracker” homogenizer. For all experiments, the percentage of hybrid vesicles labeling for TAP1-GFP and MHC class II-L243 relative to single or non-labeled vesicles was determined by a Beckman-Coulter MoFlo fluorescent cell sorter and represented in the graphs. All experiments are performed in multiplo. Shown is mean + SD. (A) Discernable cell populations with either ER (Tap1-GFP) or PM (stained MHC-II) markers were broken in separate tubes and than mixed ('Stained: Separately, Fractionated: Separately') or broken in the same tube simultaneously ('Stained: Separately, Fractionated: Together'). As a control cells labeled with both markers were used ('Stained: Together, Fractionated: Together'). (B) Fractionation strokes were performed 2, 10 or 30 times (ball size 8.010mm) or (D) with ball sizes of 8.010, 8.008 or 8.004mm (30 strokes). As a soft detergent 0.1% Triton X-100 in PBS (Triton) was used for 5 or 10 minutes on ice. (C) Sonication pulses of approximately 0.5 second by a Branson sonifier 250 (Duty cycle 50%, output control 5) or <t>Diagenode</t> <t>Bioruptor</t> (High level 0.5 seconds on/off interval), for either 4 (short), 8 (intermediate) or 12 (long) pulses. The released cell fragments were spun down and both supernatant and PBS resuspended pellets were analyzed. (E) The effect of temperature variations on formation of hybrid vesicles test was performed by EMBL cell cracker with 8.010mm ball size. Fractionation was 30 times at 4, 10, 18, 25 and 37 o C.
    Diagenode Bioruptor, supplied by Diagenode, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/diagenode bioruptor/product/Diagenode
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    diagenode bioruptor - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    86
    Diagenode bioruptor sonicator
    Quantifying hybrid particles presenting both ER and PM markers . The membrane integrity of MelJuSo cells was compromised by EMBL 8.020mm “cell cracker” homogenizer. For all experiments, the percentage of hybrid vesicles labeling for TAP1-GFP and MHC class II-L243 relative to single or non-labeled vesicles was determined by a Beckman-Coulter MoFlo fluorescent cell sorter and represented in the graphs. All experiments are performed in multiplo. Shown is mean + SD. (A) Discernable cell populations with either ER (Tap1-GFP) or PM (stained MHC-II) markers were broken in separate tubes and than mixed ('Stained: Separately, Fractionated: Separately') or broken in the same tube simultaneously ('Stained: Separately, Fractionated: Together'). As a control cells labeled with both markers were used ('Stained: Together, Fractionated: Together'). (B) Fractionation strokes were performed 2, 10 or 30 times (ball size 8.010mm) or (D) with ball sizes of 8.010, 8.008 or 8.004mm (30 strokes). As a soft detergent 0.1% Triton X-100 in PBS (Triton) was used for 5 or 10 minutes on ice. (C) Sonication pulses of approximately 0.5 second by a Branson sonifier 250 (Duty cycle 50%, output control 5) or <t>Diagenode</t> <t>Bioruptor</t> (High level 0.5 seconds on/off interval), for either 4 (short), 8 (intermediate) or 12 (long) pulses. The released cell fragments were spun down and both supernatant and PBS resuspended pellets were analyzed. (E) The effect of temperature variations on formation of hybrid vesicles test was performed by EMBL cell cracker with 8.010mm ball size. Fractionation was 30 times at 4, 10, 18, 25 and 37 o C.
    Bioruptor Sonicator, supplied by Diagenode, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioruptor sonicator/product/Diagenode
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bioruptor sonicator - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    86
    Diagenode bioruptor pico
    Sonication efficiency and antibody specificity. a Chromatin samples were fragmented at 20 sec ON/30 sec OFF using <t>Bioruptor®</t> Pico. Samples were decrosslinked, DNA was purified by phenol:chloroform:isoamyl alcohol extraction and loaded on 1.5% agarose gel. Lane 1: non-sonicated; lane 2: sonicated 7 times; lane 3: sonicated 15 times; lane 4: sonicated 20 times; lane M: 5000 bp DNA marker. Scales indicate the DNA fragments to be between 100–500 bp. b Western blot figure showing lane M: protein molecular weight marker; lane 1: crude protein extract (40 μg); lane 2: IP in sample 1; lane 3: IP in sample 2; lane 4: mock control in sample 1; lane 5: mock control in sample 2. Arrow indicates the protein marker band 50 KD. c Western blot showing the lane M protein weight marker; lane 1: crude protein extract (40 μg) from endosperms of 35 DAP castor bean seeds; lane 2: IP sample; lane 3: IP sample (20 μl from the IP sample used for lane 2); lane 4: mock control sample. Arrow indicates the protein marker band 50 KD.
    Bioruptor Pico, supplied by Diagenode, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioruptor pico/product/Diagenode
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bioruptor pico - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    Image Search Results


    Library preparation using the CapSMART method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Phosphorylation to add mono-phosphate to the non-capped 5′ end molecules using T4 Polynucleotide Kinase. D) Ligation of STOP oligos. A total of three kinds of oligonucleotides ( Table 2 : STOP1: iGiCiG, STOP2: iCiGiC, STOPMix: mixture of STOP1 and STOP2) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. H) Illumina sequencing library preparation.

    Journal: PLoS ONE

    Article Title: Four Methods of Preparing mRNA 5? End Libraries Using the Illumina Sequencing Platform

    doi: 10.1371/journal.pone.0101812

    Figure Lengend Snippet: Library preparation using the CapSMART method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Phosphorylation to add mono-phosphate to the non-capped 5′ end molecules using T4 Polynucleotide Kinase. D) Ligation of STOP oligos. A total of three kinds of oligonucleotides ( Table 2 : STOP1: iGiCiG, STOP2: iCiGiC, STOPMix: mixture of STOP1 and STOP2) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. H) Illumina sequencing library preparation.

    Article Snippet: Sonication was performed using a Bioruptor (Diagenode).

    Techniques: De-Phosphorylation Assay, Ligation, Amplification, Polymerase Chain Reaction, Sequencing

    Library preparation using the ligation method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Tobacco Acid Pyrophosphatase treatment to remove the 5′ cap structure, exposing a mono-phosphate group for subsequent ligation. D) Ligation of RNA oligomers. A total of six tags ( Table 3 : TAG02, TAG04, TAG05, TAG06, TAG07, TAG12) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor, collection of biotinylated 5′ ends using beads, and sample pooling for multiplexing. H) Illumina sequencing library preparation.

    Journal: PLoS ONE

    Article Title: Four Methods of Preparing mRNA 5? End Libraries Using the Illumina Sequencing Platform

    doi: 10.1371/journal.pone.0101812

    Figure Lengend Snippet: Library preparation using the ligation method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Tobacco Acid Pyrophosphatase treatment to remove the 5′ cap structure, exposing a mono-phosphate group for subsequent ligation. D) Ligation of RNA oligomers. A total of six tags ( Table 3 : TAG02, TAG04, TAG05, TAG06, TAG07, TAG12) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor, collection of biotinylated 5′ ends using beads, and sample pooling for multiplexing. H) Illumina sequencing library preparation.

    Article Snippet: Sonication was performed using a Bioruptor (Diagenode).

    Techniques: Ligation, De-Phosphorylation Assay, Amplification, Polymerase Chain Reaction, Multiplexing, Sequencing

    Library preparation using the Non-CapSMART method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Tobacco Acid Pyrophosphatase treatment to remove the 5′ cap structure, exposing a mono-phosphate group for subsequent ligation. D) Ligation of STOP oligos. A total of three kinds of oligonucleotides ( Table 2 : STOP1: iGiCiG, STOP2: iCiGiC, STOPMix: mixture of STOP1 and STOP2) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. H) Illumina sequencing library preparation.

    Journal: PLoS ONE

    Article Title: Four Methods of Preparing mRNA 5? End Libraries Using the Illumina Sequencing Platform

    doi: 10.1371/journal.pone.0101812

    Figure Lengend Snippet: Library preparation using the Non-CapSMART method. A) The protocol used either poly A+ (0.50–10 µg) or total (10–200 µg) RNA. B) De-phosphorylation of mono-, di-, and tri- phosphate groups from non-capped 5′ end molecules using alkaline phosphatase. C) Tobacco Acid Pyrophosphatase treatment to remove the 5′ cap structure, exposing a mono-phosphate group for subsequent ligation. D) Ligation of STOP oligos. A total of three kinds of oligonucleotides ( Table 2 : STOP1: iGiCiG, STOP2: iCiGiC, STOPMix: mixture of STOP1 and STOP2) were used in the present study. E) First-strand cDNA synthesis. F) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. G) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. H) Illumina sequencing library preparation.

    Article Snippet: Sonication was performed using a Bioruptor (Diagenode).

    Techniques: De-Phosphorylation Assay, Ligation, Amplification, Polymerase Chain Reaction, Sequencing

    Library preparation using the SMART method. A) The protocol used either poly A+ (0.025–0.5 µg) or total (0.05–1.0 µg) RNA. B) First-strand cDNA synthesis, together with template switching and continuous replication to the end of the oligonucleotide. C) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. D) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. E) Illumina sequencing library preparation.

    Journal: PLoS ONE

    Article Title: Four Methods of Preparing mRNA 5? End Libraries Using the Illumina Sequencing Platform

    doi: 10.1371/journal.pone.0101812

    Figure Lengend Snippet: Library preparation using the SMART method. A) The protocol used either poly A+ (0.025–0.5 µg) or total (0.05–1.0 µg) RNA. B) First-strand cDNA synthesis, together with template switching and continuous replication to the end of the oligonucleotide. C) Second-strand cDNA amplification by PCR with biotinylated 5′ end primers. D) Fragmentation of cDNA using a Bioruptor and collection of biotinylated 5′ ends using beads. E) Illumina sequencing library preparation.

    Article Snippet: Sonication was performed using a Bioruptor (Diagenode).

    Techniques: Amplification, Polymerase Chain Reaction, Sequencing

    Quantifying hybrid particles presenting both ER and PM markers . The membrane integrity of MelJuSo cells was compromised by EMBL 8.020mm “cell cracker” homogenizer. For all experiments, the percentage of hybrid vesicles labeling for TAP1-GFP and MHC class II-L243 relative to single or non-labeled vesicles was determined by a Beckman-Coulter MoFlo fluorescent cell sorter and represented in the graphs. All experiments are performed in multiplo. Shown is mean + SD. (A) Discernable cell populations with either ER (Tap1-GFP) or PM (stained MHC-II) markers were broken in separate tubes and than mixed ('Stained: Separately, Fractionated: Separately') or broken in the same tube simultaneously ('Stained: Separately, Fractionated: Together'). As a control cells labeled with both markers were used ('Stained: Together, Fractionated: Together'). (B) Fractionation strokes were performed 2, 10 or 30 times (ball size 8.010mm) or (D) with ball sizes of 8.010, 8.008 or 8.004mm (30 strokes). As a soft detergent 0.1% Triton X-100 in PBS (Triton) was used for 5 or 10 minutes on ice. (C) Sonication pulses of approximately 0.5 second by a Branson sonifier 250 (Duty cycle 50%, output control 5) or Diagenode Bioruptor (High level 0.5 seconds on/off interval), for either 4 (short), 8 (intermediate) or 12 (long) pulses. The released cell fragments were spun down and both supernatant and PBS resuspended pellets were analyzed. (E) The effect of temperature variations on formation of hybrid vesicles test was performed by EMBL cell cracker with 8.010mm ball size. Fractionation was 30 times at 4, 10, 18, 25 and 37 o C.

    Journal: International Journal of Biological Sciences

    Article Title: Mechanical Forces Used for Cell Fractionation Can Create Hybrid Membrane Vesicles

    doi:

    Figure Lengend Snippet: Quantifying hybrid particles presenting both ER and PM markers . The membrane integrity of MelJuSo cells was compromised by EMBL 8.020mm “cell cracker” homogenizer. For all experiments, the percentage of hybrid vesicles labeling for TAP1-GFP and MHC class II-L243 relative to single or non-labeled vesicles was determined by a Beckman-Coulter MoFlo fluorescent cell sorter and represented in the graphs. All experiments are performed in multiplo. Shown is mean + SD. (A) Discernable cell populations with either ER (Tap1-GFP) or PM (stained MHC-II) markers were broken in separate tubes and than mixed ('Stained: Separately, Fractionated: Separately') or broken in the same tube simultaneously ('Stained: Separately, Fractionated: Together'). As a control cells labeled with both markers were used ('Stained: Together, Fractionated: Together'). (B) Fractionation strokes were performed 2, 10 or 30 times (ball size 8.010mm) or (D) with ball sizes of 8.010, 8.008 or 8.004mm (30 strokes). As a soft detergent 0.1% Triton X-100 in PBS (Triton) was used for 5 or 10 minutes on ice. (C) Sonication pulses of approximately 0.5 second by a Branson sonifier 250 (Duty cycle 50%, output control 5) or Diagenode Bioruptor (High level 0.5 seconds on/off interval), for either 4 (short), 8 (intermediate) or 12 (long) pulses. The released cell fragments were spun down and both supernatant and PBS resuspended pellets were analyzed. (E) The effect of temperature variations on formation of hybrid vesicles test was performed by EMBL cell cracker with 8.010mm ball size. Fractionation was 30 times at 4, 10, 18, 25 and 37 o C.

    Article Snippet: Alternatively, cell disintegration was achieved by sonication pulses of approximately 0.5 second by a Branson sonifier 250 (Duty cycle 50%, output control 5) or Diagenode Bioruptor (High level 0.5 seconds on/off interval), for either 4 (short), 8 (intermediate) or 12 (long) pulses.

    Techniques: Labeling, Staining, Fractionation, Sonication

    Sonication efficiency and antibody specificity. a Chromatin samples were fragmented at 20 sec ON/30 sec OFF using Bioruptor® Pico. Samples were decrosslinked, DNA was purified by phenol:chloroform:isoamyl alcohol extraction and loaded on 1.5% agarose gel. Lane 1: non-sonicated; lane 2: sonicated 7 times; lane 3: sonicated 15 times; lane 4: sonicated 20 times; lane M: 5000 bp DNA marker. Scales indicate the DNA fragments to be between 100–500 bp. b Western blot figure showing lane M: protein molecular weight marker; lane 1: crude protein extract (40 μg); lane 2: IP in sample 1; lane 3: IP in sample 2; lane 4: mock control in sample 1; lane 5: mock control in sample 2. Arrow indicates the protein marker band 50 KD. c Western blot showing the lane M protein weight marker; lane 1: crude protein extract (40 μg) from endosperms of 35 DAP castor bean seeds; lane 2: IP sample; lane 3: IP sample (20 μl from the IP sample used for lane 2); lane 4: mock control sample. Arrow indicates the protein marker band 50 KD.

    Journal: PLoS ONE

    Article Title: Development of an efficient chromatin immunoprecipitation method to investigate protein-DNA interaction in oleaginous castor bean seeds

    doi: 10.1371/journal.pone.0197126

    Figure Lengend Snippet: Sonication efficiency and antibody specificity. a Chromatin samples were fragmented at 20 sec ON/30 sec OFF using Bioruptor® Pico. Samples were decrosslinked, DNA was purified by phenol:chloroform:isoamyl alcohol extraction and loaded on 1.5% agarose gel. Lane 1: non-sonicated; lane 2: sonicated 7 times; lane 3: sonicated 15 times; lane 4: sonicated 20 times; lane M: 5000 bp DNA marker. Scales indicate the DNA fragments to be between 100–500 bp. b Western blot figure showing lane M: protein molecular weight marker; lane 1: crude protein extract (40 μg); lane 2: IP in sample 1; lane 3: IP in sample 2; lane 4: mock control in sample 1; lane 5: mock control in sample 2. Arrow indicates the protein marker band 50 KD. c Western blot showing the lane M protein weight marker; lane 1: crude protein extract (40 μg) from endosperms of 35 DAP castor bean seeds; lane 2: IP sample; lane 3: IP sample (20 μl from the IP sample used for lane 2); lane 4: mock control sample. Arrow indicates the protein marker band 50 KD.

    Article Snippet: In our experiment, we tried to optimize the shearing conditions using Bioruptor® Pico (DIAGENODE, BELGIUM) with a combination of 20 sec ON/30 sec OFF for several times, and obtained maximum fragments in the range of 100–500 bp in 20 times on agarose gel ( ).

    Techniques: Sonication, Size-exclusion Chromatography, Purification, Agarose Gel Electrophoresis, Marker, Western Blot, Molecular Weight