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  • 99
    New England Biolabs monarch pcr cleanup kit
    Monarch Pcr Cleanup Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    monarch pcr cleanup kit - by Bioz Stars, 2020-05
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    90
    Thermo Fisher pcr cleanup kit
    Construction of DENV by Gibson assembly. (A) Assembly schemes of DENV infectious <t>DNA.</t> CMV, CMV promoter; HDV, HDV ribozyme; SV40PA, polyadenylation signal. (Left) Assembly scheme for DENV2-16681 and DENV4-H241; (right) assembly scheme for DENV4-v17. (B) The comparison between the foci of the original virus stocks and the foci of viruses recovered through Gibson assembly. The number of DENV <t>PCR</t> products assembled (# PCR) is shown. (C) PCR products for sequencing of virus recovered from transfected 293T cells were generated from cDNA and not contaminated assembled DNA. +, viral RNA was treated with RNase A during cDNA synthesis. (D) Comparison between sequence heterogeneities of the original v17 strain, v17 recovered by our method, and v17 cultured in C6/36 cells. The heterogeneous positions are highlighted in yellow.
    Pcr Cleanup Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick polymerase chain reaction pcr cleanup kit
    Construction of DENV by Gibson assembly. (A) Assembly schemes of DENV infectious <t>DNA.</t> CMV, CMV promoter; HDV, HDV ribozyme; SV40PA, polyadenylation signal. (Left) Assembly scheme for DENV2-16681 and DENV4-H241; (right) assembly scheme for DENV4-v17. (B) The comparison between the foci of the original virus stocks and the foci of viruses recovered through Gibson assembly. The number of DENV <t>PCR</t> products assembled (# PCR) is shown. (C) PCR products for sequencing of virus recovered from transfected 293T cells were generated from cDNA and not contaminated assembled DNA. +, viral RNA was treated with RNase A during cDNA synthesis. (D) Comparison between sequence heterogeneities of the original v17 strain, v17 recovered by our method, and v17 cultured in C6/36 cells. The heterogeneous positions are highlighted in yellow.
    Qiaquick Polymerase Chain Reaction Pcr Cleanup Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore genelute polymerase chain reaction pcr cleanup kit
    Construction of DENV by Gibson assembly. (A) Assembly schemes of DENV infectious <t>DNA.</t> CMV, CMV promoter; HDV, HDV ribozyme; SV40PA, polyadenylation signal. (Left) Assembly scheme for DENV2-16681 and DENV4-H241; (right) assembly scheme for DENV4-v17. (B) The comparison between the foci of the original virus stocks and the foci of viruses recovered through Gibson assembly. The number of DENV <t>PCR</t> products assembled (# PCR) is shown. (C) PCR products for sequencing of virus recovered from transfected 293T cells were generated from cDNA and not contaminated assembled DNA. +, viral RNA was treated with RNase A during cDNA synthesis. (D) Comparison between sequence heterogeneities of the original v17 strain, v17 recovered by our method, and v17 cultured in C6/36 cells. The heterogeneous positions are highlighted in yellow.
    Genelute Polymerase Chain Reaction Pcr Cleanup Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Axygen pcr cleanup kit
    Phenotypes of the pre6 mutants and the PRE6 overexpression plants. (A) A diagram showing the <t>T-DNA</t> insertion sites in the pre6-1 and pre6-2 mutants. (B) Expression of PRE6 transcript in the pre6 mutants ( pre6-1 and pre6-2 ) and transgenic plants overexpressing PRE6 ( 35S:PRE6-1 and 35S:PRE6-2 ). RNA was isolated from 14-day-old seedlings, and <t>RT-PCR</t> was used to examine the expression of PRE6 . The expression of ACT2 was used as a control. (C) Photographs of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Sterilized seeds were grown on vertically placed 1/2 MS plates in darkness, and photographs were taken under a microscope. (D) Hypocotyl length of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Photographs were taken under a microscope, and ImageJ software was used to measure the hypocotyl length. Data represent the mean ± SD of 33–35 seedlings. ∗ Significantly different from the Col wild type seedlings ( p
    Pcr Cleanup Kit, supplied by Axygen, used in various techniques. Bioz Stars score: 94/100, based on 432 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Promega pcr cleanup kit
    <t>PA3719</t> and MexR control of in vitro mexA transcription. (A) Impact of PA3719 on MexR repression of mexA transcription. Phage T7 RNA polymerase-based in vitro transcription reactions were initiated from a 836-bp <t>PCR-generated</t> template (250 ng) carrying a T7 promoter and mexA sequences extending from the MexR operator to 585 bp into the mexA gene (lanes 1 to 4). The results for control reactions with a T7 promoter-containing DNA template, pTRI-Xef, provided with the T7 in vitro transcription kit, are shown in lanes 5 to 7. Reactions were carried out at 37°C for 3 h, and RNA was purified and subjected to electrophoresis prior to visualization with ethidium bromide. MexR (1 μM) and PA3719 (150 nM [+ 1 ] or 500 nM [+ 2] ) were included in the reaction mixtures as indicated. Equal volumes of RNA were loaded in each instance. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 1.1 μg; lane 3, 2.0 μg; lane 4, 4.2 μg; lane 5, 1.7 μg; lane 6, 1.6 μg; and lane 7, 1.6 μg. (B) Impact of PA3719 on mexA transcription. In vitro transcription of the mex (lanes 1 to 3) and pTRI-Xef (lanes 4 to 6) templates was carried out as described above with or without PA3719 (500 nM [+ 2 ] or 2 μM [+ 3 ]), as indicated. The following amounts of RNA were produced: lane 1, 4.4 μg; lane 2, 4.5 μg; lane 3, 4.6 μg; lane 4, 4.6 μg; lane 5, 4.6 μg; and lane 6, 4.4 μg. (C) Differential impact of PA3719 on the repressor activities of MexR and MexR I104F . In vitro transcription of the mex (lanes 1 to 5) and pTRI-Xef (lanes 6 to 8) templates was carried out as described above with or without PA3719 (500 nM) and MexR/MexR I104F (1 μM), as indicated. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 0.8 μg; lane 3, 3.8 μg; lane 4, 0.9 μg; lane 5, 1.9 μg; lane 6, 6.6 μg; lane 7, 6.5 μg; and lane 8, 6.4 μg. RNA was quantitated prior to loading, and the values reported reflect the amount loaded and not the total amount produced. Because reaction, recovery, and loading volumes were kept constant throughout, these values accurately reflect the relative transcript levels produced in each instance.
    Pcr Cleanup Kit, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 439 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MACHEREY NAGEL pcr cleanup kit
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Pcr Cleanup Kit, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 95/100, based on 646 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche pcr cleanup kit
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Pcr Cleanup Kit, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    tiangen biotech co pcr cleanup kits
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Pcr Cleanup Kits, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Fisher Scientific pcr cleanup kit
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Pcr Cleanup Kit, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa pcr cleanup kit
    TGIRT ssDNA-seq workflow. The target DNA (2–50 ng in this work) is treated with alkaline phosphatase to remove 3′ phosphates and heat denatured prior to DNA-seq library construction. The resulting ssDNAs with 3′ OH termini are then used for TGIRT template-switching DNA synthesis coupled to Illumina read 2 reverse (R2R) DNA-seq adapter addition. In this novel reaction, the TGIRT-III enzyme (InGex) binds first to a synthetic 34-bp R2 RNA/R2R DNA heteroduplex in which the R2R DNA primer has a single nucleotide 3′ overhang that can direct TGIRT template switching by base pairing to the 3′ nucleotide of a target DNA strand. For minimally biased library preparation, the 3′-overhang nucleotide is an equimolar mixture of A, C, G, and T (denoted N). A 3′-blocking group (C3 spacer; 3′SpC3) is attached to the end of the R2 RNA oligonucleotide to prevent template-switching to that RNA. After the TGIRT enzyme extends the DNA primer to produce a DNA copy of the target DNA strand with an R2R adapter seamlessly linked to its 5′ end, a 5′ adenylated (App) Illumina read 1 reverse <t>(R1R)</t> adapter is added to its 3′ end by single-stranded DNA ligation using a Thermostable 5′ AppDNA/RNA ligase (New England Biolabs). In the workflow shown, an unique molecular identifier (UMI) is positioned at the 5′ end of the R1R DNA oligonucleotide. A final <t>PCR</t> step adds flow cell capture sites and barcodes for Illumina sequencing and sample multiplexing.
    Pcr Cleanup Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Merck KGaA pcr cleanup kit
    TGIRT ssDNA-seq workflow. The target DNA (2–50 ng in this work) is treated with alkaline phosphatase to remove 3′ phosphates and heat denatured prior to DNA-seq library construction. The resulting ssDNAs with 3′ OH termini are then used for TGIRT template-switching DNA synthesis coupled to Illumina read 2 reverse (R2R) DNA-seq adapter addition. In this novel reaction, the TGIRT-III enzyme (InGex) binds first to a synthetic 34-bp R2 RNA/R2R DNA heteroduplex in which the R2R DNA primer has a single nucleotide 3′ overhang that can direct TGIRT template switching by base pairing to the 3′ nucleotide of a target DNA strand. For minimally biased library preparation, the 3′-overhang nucleotide is an equimolar mixture of A, C, G, and T (denoted N). A 3′-blocking group (C3 spacer; 3′SpC3) is attached to the end of the R2 RNA oligonucleotide to prevent template-switching to that RNA. After the TGIRT enzyme extends the DNA primer to produce a DNA copy of the target DNA strand with an R2R adapter seamlessly linked to its 5′ end, a 5′ adenylated (App) Illumina read 1 reverse <t>(R1R)</t> adapter is added to its 3′ end by single-stranded DNA ligation using a Thermostable 5′ AppDNA/RNA ligase (New England Biolabs). In the workflow shown, an unique molecular identifier (UMI) is positioned at the 5′ end of the R1R DNA oligonucleotide. A final <t>PCR</t> step adds flow cell capture sites and barcodes for Illumina sequencing and sample multiplexing.
    Pcr Cleanup Kit, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 92/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen ultraclean pcr cleanup kit
    TGIRT ssDNA-seq workflow. The target DNA (2–50 ng in this work) is treated with alkaline phosphatase to remove 3′ phosphates and heat denatured prior to DNA-seq library construction. The resulting ssDNAs with 3′ OH termini are then used for TGIRT template-switching DNA synthesis coupled to Illumina read 2 reverse (R2R) DNA-seq adapter addition. In this novel reaction, the TGIRT-III enzyme (InGex) binds first to a synthetic 34-bp R2 RNA/R2R DNA heteroduplex in which the R2R DNA primer has a single nucleotide 3′ overhang that can direct TGIRT template switching by base pairing to the 3′ nucleotide of a target DNA strand. For minimally biased library preparation, the 3′-overhang nucleotide is an equimolar mixture of A, C, G, and T (denoted N). A 3′-blocking group (C3 spacer; 3′SpC3) is attached to the end of the R2 RNA oligonucleotide to prevent template-switching to that RNA. After the TGIRT enzyme extends the DNA primer to produce a DNA copy of the target DNA strand with an R2R adapter seamlessly linked to its 5′ end, a 5′ adenylated (App) Illumina read 1 reverse <t>(R1R)</t> adapter is added to its 3′ end by single-stranded DNA ligation using a Thermostable 5′ AppDNA/RNA ligase (New England Biolabs). In the workflow shown, an unique molecular identifier (UMI) is positioned at the 5′ end of the R1R DNA oligonucleotide. A final <t>PCR</t> step adds flow cell capture sites and barcodes for Illumina sequencing and sample multiplexing.
    Ultraclean Pcr Cleanup Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 233 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen pcr cleanup kit
    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
    Pcr Cleanup Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 2126 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Eppendorf AG perfectprep pcr cleanup kit
    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
    Perfectprep Pcr Cleanup Kit, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Axygen axyprep pcr cleanup kit
    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
    Axyprep Pcr Cleanup Kit, supplied by Axygen, used in various techniques. Bioz Stars score: 89/100, based on 276 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    MACHEREY NAGEL pcr cleanup purification kit
    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
    Pcr Cleanup Purification Kit, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 91/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Axygen axypreptm pcr cleanup kit
    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
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    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative <t>RT-PCR</t> analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic <t>DNA</t> samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.
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    Image Search Results


    Construction of DENV by Gibson assembly. (A) Assembly schemes of DENV infectious DNA. CMV, CMV promoter; HDV, HDV ribozyme; SV40PA, polyadenylation signal. (Left) Assembly scheme for DENV2-16681 and DENV4-H241; (right) assembly scheme for DENV4-v17. (B) The comparison between the foci of the original virus stocks and the foci of viruses recovered through Gibson assembly. The number of DENV PCR products assembled (# PCR) is shown. (C) PCR products for sequencing of virus recovered from transfected 293T cells were generated from cDNA and not contaminated assembled DNA. +, viral RNA was treated with RNase A during cDNA synthesis. (D) Comparison between sequence heterogeneities of the original v17 strain, v17 recovered by our method, and v17 cultured in C6/36 cells. The heterogeneous positions are highlighted in yellow.

    Journal: Journal of Virology

    Article Title: A Simplified Positive-Sense-RNA Virus Construction Approach That Enhances Analysis Throughput

    doi: 10.1128/JVI.02261-13

    Figure Lengend Snippet: Construction of DENV by Gibson assembly. (A) Assembly schemes of DENV infectious DNA. CMV, CMV promoter; HDV, HDV ribozyme; SV40PA, polyadenylation signal. (Left) Assembly scheme for DENV2-16681 and DENV4-H241; (right) assembly scheme for DENV4-v17. (B) The comparison between the foci of the original virus stocks and the foci of viruses recovered through Gibson assembly. The number of DENV PCR products assembled (# PCR) is shown. (C) PCR products for sequencing of virus recovered from transfected 293T cells were generated from cDNA and not contaminated assembled DNA. +, viral RNA was treated with RNase A during cDNA synthesis. (D) Comparison between sequence heterogeneities of the original v17 strain, v17 recovered by our method, and v17 cultured in C6/36 cells. The heterogeneous positions are highlighted in yellow.

    Article Snippet: All the PCR products were cleaned up using a PCR cleanup kit from Invitrogen before use in DNA assembly and sequencing.

    Techniques: Polymerase Chain Reaction, Sequencing, Transfection, Generated, Cell Culture

    Construction of a DENV library with randomized amino acids at position E1690. (A) Diagram showing how the randomization was achieved at the assembly site of two PCR products (dark gray and black) during Gibson ligation. The primer sites for PCR are depicted in letters, while the rest of DNA strands are represented by solid lines. The arrows represent the direction of repair by Phusion polymerase during the assembly reaction. (B) Chromatograms of sequences at prM847, E1690, and NS4B7016 of prM+E+NS4B virus with amino acid randomization at E1690. The randomized position in E and heterogeneous nucleotides in M and NS4B are highlighted in yellow. (C) Comparison between the foci of the DENV library (prM+LibE+NS4B) and the foci of the virus with the same genetic background without randomization at E1690 (prM+E+NS4B). The foci for each virus stock in duplicate wells are shown.

    Journal: Journal of Virology

    Article Title: A Simplified Positive-Sense-RNA Virus Construction Approach That Enhances Analysis Throughput

    doi: 10.1128/JVI.02261-13

    Figure Lengend Snippet: Construction of a DENV library with randomized amino acids at position E1690. (A) Diagram showing how the randomization was achieved at the assembly site of two PCR products (dark gray and black) during Gibson ligation. The primer sites for PCR are depicted in letters, while the rest of DNA strands are represented by solid lines. The arrows represent the direction of repair by Phusion polymerase during the assembly reaction. (B) Chromatograms of sequences at prM847, E1690, and NS4B7016 of prM+E+NS4B virus with amino acid randomization at E1690. The randomized position in E and heterogeneous nucleotides in M and NS4B are highlighted in yellow. (C) Comparison between the foci of the DENV library (prM+LibE+NS4B) and the foci of the virus with the same genetic background without randomization at E1690 (prM+E+NS4B). The foci for each virus stock in duplicate wells are shown.

    Article Snippet: All the PCR products were cleaned up using a PCR cleanup kit from Invitrogen before use in DNA assembly and sequencing.

    Techniques: Polymerase Chain Reaction, Ligation

    Phenotypes of the pre6 mutants and the PRE6 overexpression plants. (A) A diagram showing the T-DNA insertion sites in the pre6-1 and pre6-2 mutants. (B) Expression of PRE6 transcript in the pre6 mutants ( pre6-1 and pre6-2 ) and transgenic plants overexpressing PRE6 ( 35S:PRE6-1 and 35S:PRE6-2 ). RNA was isolated from 14-day-old seedlings, and RT-PCR was used to examine the expression of PRE6 . The expression of ACT2 was used as a control. (C) Photographs of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Sterilized seeds were grown on vertically placed 1/2 MS plates in darkness, and photographs were taken under a microscope. (D) Hypocotyl length of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Photographs were taken under a microscope, and ImageJ software was used to measure the hypocotyl length. Data represent the mean ± SD of 33–35 seedlings. ∗ Significantly different from the Col wild type seedlings ( p

    Journal: Frontiers in Plant Science

    Article Title: Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis

    doi: 10.3389/fpls.2017.01813

    Figure Lengend Snippet: Phenotypes of the pre6 mutants and the PRE6 overexpression plants. (A) A diagram showing the T-DNA insertion sites in the pre6-1 and pre6-2 mutants. (B) Expression of PRE6 transcript in the pre6 mutants ( pre6-1 and pre6-2 ) and transgenic plants overexpressing PRE6 ( 35S:PRE6-1 and 35S:PRE6-2 ). RNA was isolated from 14-day-old seedlings, and RT-PCR was used to examine the expression of PRE6 . The expression of ACT2 was used as a control. (C) Photographs of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Sterilized seeds were grown on vertically placed 1/2 MS plates in darkness, and photographs were taken under a microscope. (D) Hypocotyl length of the 5-day-old etiolated seedlings of the Col wild type, the pre6 mutants and the 35S:PRE6 transgenic plants. Photographs were taken under a microscope, and ImageJ software was used to measure the hypocotyl length. Data represent the mean ± SD of 33–35 seedlings. ∗ Significantly different from the Col wild type seedlings ( p

    Article Snippet: After washing, the DNA-protein cross-links obtained were reversed at 65°C for 12 h, and DNA was purified using PCR Cleanup Kit (Axygen) for PCR reactions.

    Techniques: Over Expression, Expressing, Transgenic Assay, Isolation, Reverse Transcription Polymerase Chain Reaction, Mass Spectrometry, Microscopy, Software

    PA3719 and MexR control of in vitro mexA transcription. (A) Impact of PA3719 on MexR repression of mexA transcription. Phage T7 RNA polymerase-based in vitro transcription reactions were initiated from a 836-bp PCR-generated template (250 ng) carrying a T7 promoter and mexA sequences extending from the MexR operator to 585 bp into the mexA gene (lanes 1 to 4). The results for control reactions with a T7 promoter-containing DNA template, pTRI-Xef, provided with the T7 in vitro transcription kit, are shown in lanes 5 to 7. Reactions were carried out at 37°C for 3 h, and RNA was purified and subjected to electrophoresis prior to visualization with ethidium bromide. MexR (1 μM) and PA3719 (150 nM [+ 1 ] or 500 nM [+ 2] ) were included in the reaction mixtures as indicated. Equal volumes of RNA were loaded in each instance. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 1.1 μg; lane 3, 2.0 μg; lane 4, 4.2 μg; lane 5, 1.7 μg; lane 6, 1.6 μg; and lane 7, 1.6 μg. (B) Impact of PA3719 on mexA transcription. In vitro transcription of the mex (lanes 1 to 3) and pTRI-Xef (lanes 4 to 6) templates was carried out as described above with or without PA3719 (500 nM [+ 2 ] or 2 μM [+ 3 ]), as indicated. The following amounts of RNA were produced: lane 1, 4.4 μg; lane 2, 4.5 μg; lane 3, 4.6 μg; lane 4, 4.6 μg; lane 5, 4.6 μg; and lane 6, 4.4 μg. (C) Differential impact of PA3719 on the repressor activities of MexR and MexR I104F . In vitro transcription of the mex (lanes 1 to 5) and pTRI-Xef (lanes 6 to 8) templates was carried out as described above with or without PA3719 (500 nM) and MexR/MexR I104F (1 μM), as indicated. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 0.8 μg; lane 3, 3.8 μg; lane 4, 0.9 μg; lane 5, 1.9 μg; lane 6, 6.6 μg; lane 7, 6.5 μg; and lane 8, 6.4 μg. RNA was quantitated prior to loading, and the values reported reflect the amount loaded and not the total amount produced. Because reaction, recovery, and loading volumes were kept constant throughout, these values accurately reflect the relative transcript levels produced in each instance.

    Journal: Journal of Bacteriology

    Article Title: Protein Modulator of Multidrug Efflux Gene Expression in Pseudomonas aeruginosa ▿

    doi: 10.1128/JB.00543-07

    Figure Lengend Snippet: PA3719 and MexR control of in vitro mexA transcription. (A) Impact of PA3719 on MexR repression of mexA transcription. Phage T7 RNA polymerase-based in vitro transcription reactions were initiated from a 836-bp PCR-generated template (250 ng) carrying a T7 promoter and mexA sequences extending from the MexR operator to 585 bp into the mexA gene (lanes 1 to 4). The results for control reactions with a T7 promoter-containing DNA template, pTRI-Xef, provided with the T7 in vitro transcription kit, are shown in lanes 5 to 7. Reactions were carried out at 37°C for 3 h, and RNA was purified and subjected to electrophoresis prior to visualization with ethidium bromide. MexR (1 μM) and PA3719 (150 nM [+ 1 ] or 500 nM [+ 2] ) were included in the reaction mixtures as indicated. Equal volumes of RNA were loaded in each instance. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 1.1 μg; lane 3, 2.0 μg; lane 4, 4.2 μg; lane 5, 1.7 μg; lane 6, 1.6 μg; and lane 7, 1.6 μg. (B) Impact of PA3719 on mexA transcription. In vitro transcription of the mex (lanes 1 to 3) and pTRI-Xef (lanes 4 to 6) templates was carried out as described above with or without PA3719 (500 nM [+ 2 ] or 2 μM [+ 3 ]), as indicated. The following amounts of RNA were produced: lane 1, 4.4 μg; lane 2, 4.5 μg; lane 3, 4.6 μg; lane 4, 4.6 μg; lane 5, 4.6 μg; and lane 6, 4.4 μg. (C) Differential impact of PA3719 on the repressor activities of MexR and MexR I104F . In vitro transcription of the mex (lanes 1 to 5) and pTRI-Xef (lanes 6 to 8) templates was carried out as described above with or without PA3719 (500 nM) and MexR/MexR I104F (1 μM), as indicated. The following amounts of RNA were produced: lane 1, 4.2 μg; lane 2, 0.8 μg; lane 3, 3.8 μg; lane 4, 0.9 μg; lane 5, 1.9 μg; lane 6, 6.6 μg; lane 7, 6.5 μg; and lane 8, 6.4 μg. RNA was quantitated prior to loading, and the values reported reflect the amount loaded and not the total amount produced. Because reaction, recovery, and loading volumes were kept constant throughout, these values accurately reflect the relative transcript levels produced in each instance.

    Article Snippet: Annealing was achieved by incubating 800 pmol of each oligonucleotide in T4 ligation buffer at 95°C for 3 min and allowing the reaction mixture to cool at room temperature for 5 h, after which the 3′ PA3719 DNA was purified using a gel and PCR cleanup kit (Promega).

    Techniques: In Vitro, Polymerase Chain Reaction, Generated, Purification, Electrophoresis, Produced

    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).

    Journal: Applied and Environmental Microbiology

    Article Title: Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.

    doi: 10.1128/AEM.00485-19

    Figure Lengend Snippet: Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).

    Article Snippet: DNA fragments were purified from agarose gels using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel.

    Techniques: Polymerase Chain Reaction, Amplification, Molecular Weight

    TGIRT ssDNA-seq workflow. The target DNA (2–50 ng in this work) is treated with alkaline phosphatase to remove 3′ phosphates and heat denatured prior to DNA-seq library construction. The resulting ssDNAs with 3′ OH termini are then used for TGIRT template-switching DNA synthesis coupled to Illumina read 2 reverse (R2R) DNA-seq adapter addition. In this novel reaction, the TGIRT-III enzyme (InGex) binds first to a synthetic 34-bp R2 RNA/R2R DNA heteroduplex in which the R2R DNA primer has a single nucleotide 3′ overhang that can direct TGIRT template switching by base pairing to the 3′ nucleotide of a target DNA strand. For minimally biased library preparation, the 3′-overhang nucleotide is an equimolar mixture of A, C, G, and T (denoted N). A 3′-blocking group (C3 spacer; 3′SpC3) is attached to the end of the R2 RNA oligonucleotide to prevent template-switching to that RNA. After the TGIRT enzyme extends the DNA primer to produce a DNA copy of the target DNA strand with an R2R adapter seamlessly linked to its 5′ end, a 5′ adenylated (App) Illumina read 1 reverse (R1R) adapter is added to its 3′ end by single-stranded DNA ligation using a Thermostable 5′ AppDNA/RNA ligase (New England Biolabs). In the workflow shown, an unique molecular identifier (UMI) is positioned at the 5′ end of the R1R DNA oligonucleotide. A final PCR step adds flow cell capture sites and barcodes for Illumina sequencing and sample multiplexing.

    Journal: Scientific Reports

    Article Title: Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching

    doi: 10.1038/s41598-017-09064-w

    Figure Lengend Snippet: TGIRT ssDNA-seq workflow. The target DNA (2–50 ng in this work) is treated with alkaline phosphatase to remove 3′ phosphates and heat denatured prior to DNA-seq library construction. The resulting ssDNAs with 3′ OH termini are then used for TGIRT template-switching DNA synthesis coupled to Illumina read 2 reverse (R2R) DNA-seq adapter addition. In this novel reaction, the TGIRT-III enzyme (InGex) binds first to a synthetic 34-bp R2 RNA/R2R DNA heteroduplex in which the R2R DNA primer has a single nucleotide 3′ overhang that can direct TGIRT template switching by base pairing to the 3′ nucleotide of a target DNA strand. For minimally biased library preparation, the 3′-overhang nucleotide is an equimolar mixture of A, C, G, and T (denoted N). A 3′-blocking group (C3 spacer; 3′SpC3) is attached to the end of the R2 RNA oligonucleotide to prevent template-switching to that RNA. After the TGIRT enzyme extends the DNA primer to produce a DNA copy of the target DNA strand with an R2R adapter seamlessly linked to its 5′ end, a 5′ adenylated (App) Illumina read 1 reverse (R1R) adapter is added to its 3′ end by single-stranded DNA ligation using a Thermostable 5′ AppDNA/RNA ligase (New England Biolabs). In the workflow shown, an unique molecular identifier (UMI) is positioned at the 5′ end of the R1R DNA oligonucleotide. A final PCR step adds flow cell capture sites and barcodes for Illumina sequencing and sample multiplexing.

    Article Snippet: After cleaning up by using a Nucleospin Gel and PCR cleanup kit (Clontech), a 5′App/3′-CpSp blocked R1R adapter with a 13-nt UMI at its 5′ end (denoted R1R-UMI) was ligated to the 3′ end of the cDNA by using Thermostable 5′ AppDNA/RNA Ligase as specified by manufacturer’s protocol (New England Biolabs).

    Techniques: DNA Sequencing, DNA Synthesis, Blocking Assay, DNA Ligation, Polymerase Chain Reaction, Flow Cytometry, Sequencing, Multiplexing

    Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative RT-PCR analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic DNA samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.

    Journal: Genes & Development

    Article Title: Chromatin restriction by the nucleosome remodeler Mi-2β and functional interplay with lineage-specific transcription regulators control B-cell differentiation

    doi: 10.1101/gad.321901.118

    Figure Lengend Snippet: Igh rearrangement is not dependent on Mi-2β. ( A ) Diagram of Igh locus depicting proximal and distal V , D , and J clusters tested for recombination. The five V H families are represented by white boxes, and the D , J , and C regions are shown by black boxes. Rearrangement of the most distal variable gene ( V H -558 ) and the two most proximal ( V H -Q52 and V H -7183 ) was analyzed. The initiation sites for the μ0 and Iμ germline transcripts are depicted. ( B ) Semiquantitative RT-PCR analyses for Igh germline transcripts, Chd4 , and its homolog, Chd3 , in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and samples were normalized using Gapdh expression. ( C ) VDJ rearrangement in WT and ΔChd4 Cd2 pro-B cells. ( Top ) Normalized genomic DNA samples from sorted pro-B populations were analyzed for rearrangement by PCR amplification followed by Southern blotting. Fivefold dilutions of gDNA were used for PCR amplification. Rearrangement of D-J as well as V H 558 , V H -Q52 , and V H -7183 to DJ , respectively, is shown for both WT and ΔChd4 Cd2 . ( Bottom ) The deletion of the ATPase subunit of Mi-2β ( CHD4 ) was verified by PCR amplification of exons 11–23. The samples were normalized to an amplified Ikzf1 fragment. ( D ) Flow cytometry for expression of intracellular IgM ( ICμ ) in pro-B and small pre-B cells from WT and ΔChd4 Cd2 mice. Numbers indicate the percentage of cells in the ICμ -high gate. ( E ) Semiquantitative RT-PCR analyses for early B-cell differentiation markers ( Flt3 , Il7r , Ebf1 , and Pax5 ), key regulators for Ig recombination, and pre-BCR complex components ( Rag1 , Rag2 , Dntt , Vpreb1 , and Igll1 ) in pro-B cells from WT and ΔChd4 Cd2 mice. Fivefold dilutions of cDNA were used, and the samples were normalized using Gapdh expression.

    Article Snippet: Amplified DNA was purified with a Qiagen PCR cleanup kit.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Mouse Assay, Expressing, Polymerase Chain Reaction, Amplification, Southern Blot, Flow Cytometry, Cytometry, Cell Differentiation

    PCR products from amplification with OMPf (upper panel) and BMSf (lower panel) primers of genomic extracts of CO-oxidizing cultures. Products were visualized with ethidium bromide after gel electrophoresis using 1% agarose. Lanes A and L contain a 100-bp ladder (Promega, Inc.); 500- and 1,500-bp markers are indicated by arrows on the right side of the upper panel. Lane B, Oligotropha carboxidotropha ; lane C, M. smegmatis ; lane D, M. avium ; lane E, B. fungorum LB400; lane F, Stappia stellulata ; lane G, Mesorhizobium sp. strain NMB1; lane H, Bradyrhizobium sp. strain CPP; lane I, Aminobacter sp. strain COX; lane J, L. anuloederans ; lane K, negative control.

    Journal: Applied and Environmental Microbiology

    Article Title: Molecular and Culture-Based Analyses of Aerobic Carbon Monoxide Oxidizer Diversity+

    doi: 10.1128/AEM.69.12.7257-7265.2003

    Figure Lengend Snippet: PCR products from amplification with OMPf (upper panel) and BMSf (lower panel) primers of genomic extracts of CO-oxidizing cultures. Products were visualized with ethidium bromide after gel electrophoresis using 1% agarose. Lanes A and L contain a 100-bp ladder (Promega, Inc.); 500- and 1,500-bp markers are indicated by arrows on the right side of the upper panel. Lane B, Oligotropha carboxidotropha ; lane C, M. smegmatis ; lane D, M. avium ; lane E, B. fungorum LB400; lane F, Stappia stellulata ; lane G, Mesorhizobium sp. strain NMB1; lane H, Bradyrhizobium sp. strain CPP; lane I, Aminobacter sp. strain COX; lane J, L. anuloederans ; lane K, negative control.

    Article Snippet: PCR products were visualized with ethidium bromide gel electrophoresis and then purified with MoBio PCR cleanup kits.

    Techniques: Polymerase Chain Reaction, Amplification, Nucleic Acid Electrophoresis, Conditioned Place Preference, Negative Control