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  • 99
    New England Biolabs monarch dna gel extraction kit
    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic <t>DNA.</t> Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) <t>PCR</t> evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Monarch Dna Gel Extraction Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 834 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher genejet gel extraction kit
    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic <t>DNA.</t> Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) <t>PCR</t> evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Genejet Gel Extraction Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7405 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick gel extraction kit
    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic <t>DNA.</t> Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) <t>PCR</t> evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 33156 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaex ii gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Qiaex Ii Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 12750 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Axygen axyprep dna gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Axyprep Dna Gel Extraction Kit, supplied by Axygen, used in various techniques. Bioz Stars score: 94/100, based on 6483 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qia quick gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Qia Quick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 3559 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Omega Bio-tek gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Gel Extraction Kit, supplied by Omega Bio-tek, used in various techniques. Bioz Stars score: 94/100, based on 2584 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher purelink quick gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Purelink Quick Gel Extraction Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 2300 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore genelute gel extraction kit
    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For <t>gel</t> source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by <t>qRT-PCR</t> in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P
    Genelute Gel Extraction Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 2222 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Axygen dna gel extraction kit
    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 <t>DNA</t> marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of <t>QT5-19/B05.10,</t> QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.
    Dna Gel Extraction Kit, supplied by Axygen, used in various techniques. Bioz Stars score: 94/100, based on 1781 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Nippon Genetics fastgene gel pcr extraction kit
    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 <t>DNA</t> marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of <t>QT5-19/B05.10,</t> QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.
    Fastgene Gel Pcr Extraction Kit, supplied by Nippon Genetics, used in various techniques. Bioz Stars score: 90/100, based on 772 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher gel extraction kit
    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 <t>DNA</t> marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of <t>QT5-19/B05.10,</t> QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.
    Gel Extraction Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1416 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tiangen biotech co gel extraction kit
    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 <t>DNA</t> marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of <t>QT5-19/B05.10,</t> QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.
    Gel Extraction Kit, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 94/100, based on 1264 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Axygen gel extraction kit
    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 <t>DNA</t> marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of <t>QT5-19/B05.10,</t> QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.
    Gel Extraction Kit, supplied by Axygen, used in various techniques. Bioz Stars score: 94/100, based on 1184 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Journal: Frontiers in Microbiology

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior

    doi: 10.3389/fmicb.2018.01569

    Figure Lengend Snippet: CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Article Snippet: All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively.

    Techniques: CRISPR, Introduce, Sequencing, Polymerase Chain Reaction, Amplification

    Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For gel source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by qRT-PCR in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P

    Journal: Nature

    Article Title: Phosphatidylinositol 3-Kinase (PI3K) δ blockade increases genomic instability in B cells

    doi: 10.1038/nature21406

    Figure Lengend Snippet: Ibrutinib increases AID expression and the frequency of translocations to AID on- and off-target sites in mouse activated B cells a , AKT phosphorylation was detected by Western Blot in mouse activated B cells treated with DMSO, idelalisib, duvelisib or ibrutinib (1 μM) for the indicated time points (n = 2 biological replicates). For gel source data, see Supplementary Figure 1 . b , MEC1 and Mino human lymphoma cells were treated with the indicated inhibitors (1 μM) and AKT phosphorylation was evaluated by Western Blot (n = 3 biological replicates). c, Viable cells were counted at the indicated time points by Trypan Blue exclusion in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n=3). P values calculated by two-tailed Student’s t -test. d, Western blot for AID protein expression in activated B cells treated with 1 μM ibrutinib. The DMSO panel from Fig. 1a is shown for comparison (n=3 biological replicates). e, Aicda mRNA levels analyzed by qRT-PCR in activated B cells treated with DMSO or ibrutinib (1 μM). Data are expressed as mean ± s.d. (n = 3 technical replicates, n = 3 biological replicates). * P

    Article Snippet: Amplification products were purified using PCR purification kit (QIAGEN) and GEL extraction kit (QIAGEN) following the manufacturer’s protocol and sequenced bi-directionally in a Mi-Seq (Illumina NS500) sequencing platform at the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

    Techniques: Expressing, Western Blot, Two Tailed Test, Quantitative RT-PCR

    PI3Kδ inhibitors and ibrutinib increase c-myc DSB formation and the incidence of plasma cell (PC) tumor in mice a, Detailed view of the distribution of rearrangements (deletions or inversions) in the c-myc locus in mice treated as above. Numbers of translocation junctions in focal clusters are indicated in bold. b , RPM Frequency of rearrangements (deletions or inversions) in the c-myc locus in GC B cell from mice treated in vivo with the idelalisib or duvelisib. Junctions within ±300 bp of primer region were excluded. Significance is calculated as false discovery rate ( FDR ) by comparing idelalisib or duvelisib to DMSO treated mouse as indicated in the Methods. ** FDR ≤ 0.01. c , Schematic representation of the experimental outline of pristane-induced PCT in mice treated with PI3Kδ inhibitors and ibrutinib. The mice were treated in two independent biological experimental replicates, each consisting of 6 mice per group. d, Direct PCR assay for Igh/c-myc translocation in mice with PC tumors. Translocations from c-myc to the IgHα locus are shown. Translocations for the only mouse in the vehicle group and from three example mice from treated groups are shown. Bands were purified from gels and were sequenced to confirm the Igh/c-myc translocation junction. For gel source data, see Supplementary Figure 1 . e, Development of PC tumor in mice induced with pristane and treated with idelalisib, duvelisib or ibrutinib is plotted over time. The presence of PC tumors was confirmed by histology (n = 12 for each treatment in 2 independent cohorts of 6 mice). P values calculated by Log-rank (Mantel-Cox) test. f , Example histology of PC tumors in mice induced with pristane and treated with the indicated drugs. Magnification 40x; Scale bar = 50μm; Insets: high magnification image of clusters of atypical plasma cells.

    Journal: Nature

    Article Title: Phosphatidylinositol 3-Kinase (PI3K) δ blockade increases genomic instability in B cells

    doi: 10.1038/nature21406

    Figure Lengend Snippet: PI3Kδ inhibitors and ibrutinib increase c-myc DSB formation and the incidence of plasma cell (PC) tumor in mice a, Detailed view of the distribution of rearrangements (deletions or inversions) in the c-myc locus in mice treated as above. Numbers of translocation junctions in focal clusters are indicated in bold. b , RPM Frequency of rearrangements (deletions or inversions) in the c-myc locus in GC B cell from mice treated in vivo with the idelalisib or duvelisib. Junctions within ±300 bp of primer region were excluded. Significance is calculated as false discovery rate ( FDR ) by comparing idelalisib or duvelisib to DMSO treated mouse as indicated in the Methods. ** FDR ≤ 0.01. c , Schematic representation of the experimental outline of pristane-induced PCT in mice treated with PI3Kδ inhibitors and ibrutinib. The mice were treated in two independent biological experimental replicates, each consisting of 6 mice per group. d, Direct PCR assay for Igh/c-myc translocation in mice with PC tumors. Translocations from c-myc to the IgHα locus are shown. Translocations for the only mouse in the vehicle group and from three example mice from treated groups are shown. Bands were purified from gels and were sequenced to confirm the Igh/c-myc translocation junction. For gel source data, see Supplementary Figure 1 . e, Development of PC tumor in mice induced with pristane and treated with idelalisib, duvelisib or ibrutinib is plotted over time. The presence of PC tumors was confirmed by histology (n = 12 for each treatment in 2 independent cohorts of 6 mice). P values calculated by Log-rank (Mantel-Cox) test. f , Example histology of PC tumors in mice induced with pristane and treated with the indicated drugs. Magnification 40x; Scale bar = 50μm; Insets: high magnification image of clusters of atypical plasma cells.

    Article Snippet: Amplification products were purified using PCR purification kit (QIAGEN) and GEL extraction kit (QIAGEN) following the manufacturer’s protocol and sequenced bi-directionally in a Mi-Seq (Illumina NS500) sequencing platform at the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

    Techniques: Mouse Assay, Translocation Assay, In Vivo, Polymerase Chain Reaction, Purification

    Phosphatidylinositol 3-Kinase (PI3K)δ blockade increases AID expression and CSR in activated mouse B cells a , Western blot for AID protein from B cells treated with the indicated inhibitors (1 μM) (n = 3 biological replicates). For gel source data, see Supplementary Figure 1 . b , Aicda mRNA levels were analyzed by qRT-PCR. Data are expressed as mean ± s.d. (n = 3 biological replicates).. ** P ≤ 0.01, *** P ≤ 0.001, two-tailed Student’s t -test from idelalisib or duvelisib vs DMSO-treated B cells. c, GRO-Seq profiles of Aicda gene in B cells at 48 h after activation (n = 2 biological replicates). Blue profiles: sense transcription, Red profiles: antisense transcription. d, Quantification of GRO-Seq sense and antisense reads per kilobase per million mapped reads (RPKM) in the Aicda gene, ** P ≤ 0.01 ,***P ≤ 0.001, multiple test adjusted. e, IgG 1 CSR in activated B cells. Data are expressed as mean ± s.d. (n = 3 biological replicates). ** P ≤ 0.01, *** P ≤ 0.001, two-tailed Student’s t -test from idelalisib or duvelisib vs DMSO treated B cells

    Journal: Nature

    Article Title: Phosphatidylinositol 3-Kinase (PI3K) δ blockade increases genomic instability in B cells

    doi: 10.1038/nature21406

    Figure Lengend Snippet: Phosphatidylinositol 3-Kinase (PI3K)δ blockade increases AID expression and CSR in activated mouse B cells a , Western blot for AID protein from B cells treated with the indicated inhibitors (1 μM) (n = 3 biological replicates). For gel source data, see Supplementary Figure 1 . b , Aicda mRNA levels were analyzed by qRT-PCR. Data are expressed as mean ± s.d. (n = 3 biological replicates).. ** P ≤ 0.01, *** P ≤ 0.001, two-tailed Student’s t -test from idelalisib or duvelisib vs DMSO-treated B cells. c, GRO-Seq profiles of Aicda gene in B cells at 48 h after activation (n = 2 biological replicates). Blue profiles: sense transcription, Red profiles: antisense transcription. d, Quantification of GRO-Seq sense and antisense reads per kilobase per million mapped reads (RPKM) in the Aicda gene, ** P ≤ 0.01 ,***P ≤ 0.001, multiple test adjusted. e, IgG 1 CSR in activated B cells. Data are expressed as mean ± s.d. (n = 3 biological replicates). ** P ≤ 0.01, *** P ≤ 0.001, two-tailed Student’s t -test from idelalisib or duvelisib vs DMSO treated B cells

    Article Snippet: Amplification products were purified using PCR purification kit (QIAGEN) and GEL extraction kit (QIAGEN) following the manufacturer’s protocol and sequenced bi-directionally in a Mi-Seq (Illumina NS500) sequencing platform at the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

    Techniques: Expressing, Western Blot, Quantitative RT-PCR, Two Tailed Test, Activation Assay

    Detection of E2F1 variants in tissue A. PCR amplification of E2F1 variants in indicated tissues, using exon 1 and 7 primers. Products visualized on agarose gel at low (top) and high (bottom) contrast. Note the presence of three separate products in the cortex sample corresponding to E2F1a, E2F1b, and E2F1c variants. Only E2F1a is present in the other tissues. B. PCR targeting only the E2F1b variant (exon 1 and intron 5), only detected in cortex. C. PCR for E2F1 variants as in A , using exon 4 and 7 primers. Note three bands present in the cortex sample, corresponding to E2F1a, E2F1b, and E2F1c variants. Only E2F1a was detected in all other tissues. All gels are representative of PCRs from at least n = 4 biological samples. PCRs performed on cDNA generated from DNase digested RNA. All PCR products for E2F1b and E2F1c variants were gel extracted and validated by DNA sequencing. Equal loading of RNA for cDNA synthesis and subsequent PCR reactions was confirmed by a PCR reaction for GAPDH (data not shown).

    Journal: Molecular and cellular neurosciences

    Article Title: Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS

    doi: 10.1016/j.mcn.2018.06.003

    Figure Lengend Snippet: Detection of E2F1 variants in tissue A. PCR amplification of E2F1 variants in indicated tissues, using exon 1 and 7 primers. Products visualized on agarose gel at low (top) and high (bottom) contrast. Note the presence of three separate products in the cortex sample corresponding to E2F1a, E2F1b, and E2F1c variants. Only E2F1a is present in the other tissues. B. PCR targeting only the E2F1b variant (exon 1 and intron 5), only detected in cortex. C. PCR for E2F1 variants as in A , using exon 4 and 7 primers. Note three bands present in the cortex sample, corresponding to E2F1a, E2F1b, and E2F1c variants. Only E2F1a was detected in all other tissues. All gels are representative of PCRs from at least n = 4 biological samples. PCRs performed on cDNA generated from DNase digested RNA. All PCR products for E2F1b and E2F1c variants were gel extracted and validated by DNA sequencing. Equal loading of RNA for cDNA synthesis and subsequent PCR reactions was confirmed by a PCR reaction for GAPDH (data not shown).

    Article Snippet: For DNA sequencing of PCR products, DNA was gel extracted using the Qiagen DNA gel extraction kit (Qiagen) according to the manufacturers recommendations.

    Techniques: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Variant Assay, Generated, DNA Sequencing

    E2F1 variants among neuronal cell types. A. E2F1 variants amplified with common primers (exons 4 and 7) or primers specific to E2F1b (intron 5, exon 7). B. Only E2F1a was detected in Rat2 fibroblasts when cells were asynchronous or arrested in G 0 /G 1 phase, S phase, and M phase. Full length genomic E2F1 sequence amplified via PCR using genomic DNA; banding pattern was distinct from the three transcripts present in cortical neurons. PCR for GAPDH (bottom) indicates equal loading between samples. Images are representative of n = 3 separate experiments.

    Journal: Molecular and cellular neurosciences

    Article Title: Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS

    doi: 10.1016/j.mcn.2018.06.003

    Figure Lengend Snippet: E2F1 variants among neuronal cell types. A. E2F1 variants amplified with common primers (exons 4 and 7) or primers specific to E2F1b (intron 5, exon 7). B. Only E2F1a was detected in Rat2 fibroblasts when cells were asynchronous or arrested in G 0 /G 1 phase, S phase, and M phase. Full length genomic E2F1 sequence amplified via PCR using genomic DNA; banding pattern was distinct from the three transcripts present in cortical neurons. PCR for GAPDH (bottom) indicates equal loading between samples. Images are representative of n = 3 separate experiments.

    Article Snippet: For DNA sequencing of PCR products, DNA was gel extracted using the Qiagen DNA gel extraction kit (Qiagen) according to the manufacturers recommendations.

    Techniques: Amplification, Sequencing, Polymerase Chain Reaction

    PCR amplification of E2F1 alternative splice variants from rat cortex. A. Amplification of E2F1 variants using primers against exons 1 and 7, note three different product sizes (arrows) corresponding to E2F1a (middle), E2F1b (top) and E2F1c (bottom). Low (left) and high (right) contrasts of the same gel are shown. DNA from all three bands was gel extracted and confirmed by DNA sequencing. B. Amplification of E2F1 variants in rat cortex with primers against exons 4 and 7, showing three different size products: E2F1a (middle), E2F1b (top) and E2F1c (bottom). Gels from two separate experiments are shown to convey variation in relative E2F1 variant abundance. DNA from all three products was gel extracted and verified by sequencing. C. PCR targeting E2F1b only, using a forward primer specific to intron 5 and a common reverse primer. D. PCR specifically targeting E2F1b, using a common forward primer and a primer specific for intron 5. All gels are representative of PCRs from at least n = 4 biologically different samples. E. PCR with a forward primer spanning the exon 5/6 junction and the exon 7 reverse primer, amplifying E2F1a (lane 1), or with a forward primer spanning the exon 5/7 junction (only present when exon 6 deleted) and the exon 7 reverse primer, amplifying E2F1c (lane 2).

    Journal: Molecular and cellular neurosciences

    Article Title: Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS

    doi: 10.1016/j.mcn.2018.06.003

    Figure Lengend Snippet: PCR amplification of E2F1 alternative splice variants from rat cortex. A. Amplification of E2F1 variants using primers against exons 1 and 7, note three different product sizes (arrows) corresponding to E2F1a (middle), E2F1b (top) and E2F1c (bottom). Low (left) and high (right) contrasts of the same gel are shown. DNA from all three bands was gel extracted and confirmed by DNA sequencing. B. Amplification of E2F1 variants in rat cortex with primers against exons 4 and 7, showing three different size products: E2F1a (middle), E2F1b (top) and E2F1c (bottom). Gels from two separate experiments are shown to convey variation in relative E2F1 variant abundance. DNA from all three products was gel extracted and verified by sequencing. C. PCR targeting E2F1b only, using a forward primer specific to intron 5 and a common reverse primer. D. PCR specifically targeting E2F1b, using a common forward primer and a primer specific for intron 5. All gels are representative of PCRs from at least n = 4 biologically different samples. E. PCR with a forward primer spanning the exon 5/6 junction and the exon 7 reverse primer, amplifying E2F1a (lane 1), or with a forward primer spanning the exon 5/7 junction (only present when exon 6 deleted) and the exon 7 reverse primer, amplifying E2F1c (lane 2).

    Article Snippet: For DNA sequencing of PCR products, DNA was gel extracted using the Qiagen DNA gel extraction kit (Qiagen) according to the manufacturers recommendations.

    Techniques: Polymerase Chain Reaction, Amplification, DNA Sequencing, Variant Assay, Sequencing

    Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 DNA marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of QT5-19/B05.10, QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.

    Journal: Viruses

    Article Title: A Novel Partitivirus in the Hypovirulent Isolate QT5-19 of the Plant Pathogenic Fungus Botrytis cinerea

    doi: 10.3390/v11010024

    Figure Lengend Snippet: Detection of BcPV2 in different isolates of Botrytis cinerea by dsRNA profiling and RT-PCR with specific primers. M = DL5000 DNA marker (TaKaRa). Isolates B05.10T, 08168T, XN-1T, and RoseBc-3T were derived from B05.10, 08168, XN-1 and RoseBc-3 in the pairing cultures of QT5-19/B05.10, QT5-19/08168, QT5-19/XN-1 and QT5-19/RoseBc-3, respectively.

    Article Snippet: The dsRNAs extracted from isolate QT5-19 were purified from an agarose gel after electrophoresis using Axygen® DNA gel extraction kit (Axygen® Scientific Inc., Union City, CA, USA).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Marker, Derivative Assay