top10 bacteria  (Thermo Fisher)


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    Structured Review

    Thermo Fisher top10 bacteria
    Top10 Bacteria, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/top10 bacteria/product/Thermo Fisher
    Average 99 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    top10 bacteria - by Bioz Stars, 2020-03
    99/100 stars

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    Related Articles

    Methylation Sequencing:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Paragraph title: Bisulfite-sequencing and combined bisulfite-restriction analysis (COBRA) ... Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Clone Assay:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: .. VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones. .. Sequencing on both strands was performed using the big dye terminator cycle sequencing kit (Applied Biosystems).

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: In addition to luciferase expression, in a subset of clones’ green fluorescent protein (GFP) expression was also captured using confocal microscopy (Olympus Fluoview v2.0b). .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: .. The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. The insert was fully sequenced and then recombined into the pDEST-17 bacterial expression vector using the Gateway system (Invitrogen).

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: Paragraph title: Screening for tester-specific clones ... TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. To proceed with the fusion of eGFP sequences to their vectors (pApo, pIFN and pIA respectively), both plasmids were digested with the appropriate enzymes (New England Biolabs, UK) for each case.

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. .. Cloned plasmid inserts were then purified by alkaline lysis extraction (QIAGEN) and sequenced with the M13 reverse primer by the Duke University DNA Sequencing Facility.

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Article Title: Among B cell non-Hodgkin's lymphomas, MALT lymphomas express a unique antibody repertoire with frequent rheumatoid factor reactivity
    Article Snippet: .. Cloning and sequencing IgV RT-PCR products of MALT lymphomas were either directly sequenced or cloned into pTOPO-TA-vectors and transformed into TOP10 bacteria (Invitrogen), to generate molecular IgV clones. .. Sequencing on both strands was performed by an ABI sequencer (Applied Biosystems) using the big dye-terminator cycle-sequencing kit.

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems). .. To determine the germline genes used in the IgVH -DH -JH rearrangements, the somatic IgVH mutations therein, and the IgVH -CDR3 amino acid sequence lengths, the sequences were compared with published germline IgVH genes using the Vbase database ( ) and DNAplot online (MRC Centre for Protein Engineering; ).

    Amplification:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: Paragraph title: IgVH amplification by RT-PCR, cloning, and sequencing. ... VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones.

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: DMRs of imprinted-genes were amplified by nested PCR using bisulfite treated gDNA and specific primers ( ). .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: His-MBD production A fragment of MBD1 coding for amino acids 1 to 69 was amplified by PCR from human cDNA synthesized from M091 total RNA. .. The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen).

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: Enriched tester DNA was ligated to oligonucleotides N5 and A5 (see above) and amplified with S5 as described. .. TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ).

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. To proceed with the fusion of eGFP sequences to their vectors (pApo, pIFN and pIA respectively), both plasmids were digested with the appropriate enzymes (New England Biolabs, UK) for each case.

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: The PCR program for the amplification of γ-satellite DNA was: 98°C, 2 min, 28 cycles of 98°C, 30 s, 66°C, 30 s, and 72°C, 30 s and termination by 72°C for 10 min. PCR products were electrophoresed over 0.8% agarose gels and transferred to nylon membranes (PerkinElmer; reference ). .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer.

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: From cDNA of naive and MZ B cells, IgM-VH3 transcripts were amplified using a VH3 family–specific leader primer in combination with a Cμ primer, and from memory B cells, IgG-VH3 transcripts were amplified using a VH3 family–specific leader primer in combination with a Cγ primer ( ). .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems).

    Positive Control:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: The pNL4-3 and pMJ4 were used as positive control for X4- and R5-tropic strains respectively. .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Synthesized:

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: His-MBD production A fragment of MBD1 coding for amino acids 1 to 69 was amplified by PCR from human cDNA synthesized from M091 total RNA. .. The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen).

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: IFNα plasmid (pIFN), ApoAI plasmid (pApoAI) and IFNα bound to ApoAI plasmid (pIFNApoAI) had been previously synthesized in the laboratory . .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification.

    TA Cloning:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The plasmids were prepared using a QIAprep Spin Miniprep Kit (Qiagen Inc) and sequenced with M13 forward and reverse primers.

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Construct:

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions. .. The purified proteins were concentrated with Amicon Ultra-15 centrifugal filters (MWCO 10,000, Millipore, MA), dialyzed against 100mM sodium phosphate buffer, pH 7.4 and stored at 4°C.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The digested plasmid and DmBCA-GFP construct were purified and then ligated overnight at +4°C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Incubation:

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. PCR products for sequencing were precipitated with 26 µL sequencing precipitation solution (120 mM C2 H3 O2 Na in 95% absolute ethanol), incubated for 10 min at room temperature and centrifuged at 3,000× g for 20 min.

    Luciferase:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: In addition to luciferase expression, in a subset of clones’ green fluorescent protein (GFP) expression was also captured using confocal microscopy (Olympus Fluoview v2.0b). .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Activity Assay:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: In cPTT co-receptor tropism was determined by measuring Renilla luciferase activity (relative light units [RLU]) using Bright - Glo ™ Luciferase Assay System (Promega, US). .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Expressing:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: In addition to luciferase expression, in a subset of clones’ green fluorescent protein (GFP) expression was also captured using confocal microscopy (Olympus Fluoview v2.0b). .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. The insert was fully sequenced and then recombined into the pDEST-17 bacterial expression vector using the Gateway system (Invitrogen).

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions. .. The purified proteins were concentrated with Amicon Ultra-15 centrifugal filters (MWCO 10,000, Millipore, MA), dialyzed against 100mM sodium phosphate buffer, pH 7.4 and stored at 4°C.

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. To proceed with the fusion of eGFP sequences to their vectors (pApo, pIFN and pIA respectively), both plasmids were digested with the appropriate enzymes (New England Biolabs, UK) for each case.

    Modification:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Next, 100 ng of gDNA were used in bisulfite modification, performed using the EpiTect Bisulfite Kit (Qiagen Inc) according to the manufacturer's instructions. .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Transformation Assay:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: .. VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones. .. Sequencing on both strands was performed using the big dye terminator cycle sequencing kit (Applied Biosystems).

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The plasmids were prepared using a QIAprep Spin Miniprep Kit (Qiagen Inc) and sequenced with M13 forward and reverse primers.

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity. .. The tropism was inferred by using serial dilutions of the CCR5 antagonist TAK-779 (obtained through the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, Bethesda, MD, USA) or the CXCR4 inhibitor AMD3100 (Sigma-Aldrich, St. Louis, MO, USA). rPhenotyping was compared with pGTT while cPTT were compared with cGTT.

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: .. TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions. .. The purified proteins were concentrated with Amicon Ultra-15 centrifugal filters (MWCO 10,000, Millipore, MA), dialyzed against 100mM sodium phosphate buffer, pH 7.4 and stored at 4°C.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland). .. Overnight cultures (8 ml) were made from these colonies, and plasmids were purified using a QIAprep Spin Miniprep Kit™ (Qiagen, Hilden, Germany).

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. To proceed with the fusion of eGFP sequences to their vectors (pApo, pIFN and pIA respectively), both plasmids were digested with the appropriate enzymes (New England Biolabs, UK) for each case.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: .. The ligated product was transformed into TOP10 bacteria (Invitrogen). .. Overnight cultures (8 ml) were made from these colonies, and plasmids were purified using a QIAprep Spin Miniprep Kit™ (Qiagen, Hilden, Germany).

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. ..

    Article Title: Among B cell non-Hodgkin's lymphomas, MALT lymphomas express a unique antibody repertoire with frequent rheumatoid factor reactivity
    Article Snippet: .. Cloning and sequencing IgV RT-PCR products of MALT lymphomas were either directly sequenced or cloned into pTOPO-TA-vectors and transformed into TOP10 bacteria (Invitrogen), to generate molecular IgV clones. .. Sequencing on both strands was performed by an ABI sequencer (Applied Biosystems) using the big dye-terminator cycle-sequencing kit.

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems). .. To determine the germline genes used in the IgVH -DH -JH rearrangements, the somatic IgVH mutations therein, and the IgVH -CDR3 amino acid sequence lengths, the sequences were compared with published germline IgVH genes using the Vbase database ( ) and DNAplot online (MRC Centre for Protein Engineering; ).

    Derivative Assay:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: In brief, genomic DNA were prepared from double-sorted VSELs, HSCs, STs, ESC-D3s, and cells derived from VSEL-DSs (2×104 ) using the DNeasy Blood & Tissue Kit (Qiagen Inc, Valencia, CA, USA). .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Hybridization:

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: LM-PCR products containing γ-satellite DNA were detected by hybridization ( , ) with a 32 P-labeled probe (BW-LCγ: 5′-GGAATCGCCAGACCACTGTAGGACCTGGAA-3′) that overlaps the BW-LC linker and a portion of the 234-bp γ-satellite repeat ( ); hybridization was quantitated in a Storm phosphoimager (Amersham Biosciences). .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer.

    Sequencing:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: Paragraph title: IgVH amplification by RT-PCR, cloning, and sequencing. ... VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The reverse primer also contained the nucleotide sequence encoding thrombin cleavage site. .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: Paragraph title: Sirt2 KO mutation sequencing ... The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The extra sequence overlaps at the 3' end of DmBCA and at the 5' end of the GFP allowed these PCR products to anneal to each other. .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Article Title: Among B cell non-Hodgkin's lymphomas, MALT lymphomas express a unique antibody repertoire with frequent rheumatoid factor reactivity
    Article Snippet: .. Cloning and sequencing IgV RT-PCR products of MALT lymphomas were either directly sequenced or cloned into pTOPO-TA-vectors and transformed into TOP10 bacteria (Invitrogen), to generate molecular IgV clones. .. Sequencing on both strands was performed by an ABI sequencer (Applied Biosystems) using the big dye-terminator cycle-sequencing kit.

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems). .. To determine the germline genes used in the IgVH -DH -JH rearrangements, the somatic IgVH mutations therein, and the IgVH -CDR3 amino acid sequence lengths, the sequences were compared with published germline IgVH genes using the Vbase database ( ) and DNAplot online (MRC Centre for Protein Engineering; ).

    Ligation:

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: .. TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. Afterwards, the open plasmids and their purified inserts were fused using T4 DNA ligase High Concentration and 2X Rapid Ligation Buffer (Promega, Madison, WI, USA).

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: Paragraph title: Ligation-mediated PCR. ... TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer.

    Infection:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: The rPhenotyping was performed with 31 patients’ samples infected with HIV-1C and four QC-samples. .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Generated:

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: Expression constructs were generated by inserting PCR-amplified fragments of super ecliptic pHluorin or super ecliptic pHluorin A227D cDNA into the pCR4Blunt TOPO vector (Invitrogen, NY). .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions.

    DNA Sequencing:

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. .. Cloned plasmid inserts were then purified by alkaline lysis extraction (QIAGEN) and sequenced with the M13 reverse primer by the Duke University DNA Sequencing Facility.

    Polymerase Chain Reaction:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: The PCR was performed in 1.5 mmol/l MgCl2 using Platinum Taq polymerase and PCR buffers (Invitrogen) according to the manufacturer's description. .. VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones.

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The plasmids were prepared using a QIAprep Spin Miniprep Kit (Qiagen Inc) and sequenced with M13 forward and reverse primers.

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: .. The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. The insert was fully sequenced and then recombined into the pDEST-17 bacterial expression vector using the Gateway system (Invitrogen).

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: .. TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: Expression constructs were generated by inserting PCR-amplified fragments of super ecliptic pHluorin or super ecliptic pHluorin A227D cDNA into the pCR4Blunt TOPO vector (Invitrogen, NY). .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The digested plasmid and PCR product containing full-length recombinant A. gambiae β-CA gene were purified and then ligated overnight at +4 °C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: PCR amplifications were carried out with the selected primers (listed ). .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The PCR product was run on an agarose gel, and the obtained band was purified. pFastBac™ 1 plasmid (Invitrogen) and the PCR product were digested at +37°C overnight with BamHI and XhoI restriction enzymes (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: Paragraph title: Ligation-mediated PCR. ... TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer.

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: In gene scanning experiments, a fluorochrome-labeled Cμ was used to enable automatic detection of PCR product lengths ( ). .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems).

    Sonication:

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. Inclusion bodies were sonicated briefly and washed in 1 M Urea, 20 mM Tris-Cl pH 8, 10 mM β-mercaptoethanol, 2% Triton X-100 prior to solubilization in Denaturation Buffer (8 M Urea, 20 mM Tris pH 8, 5 mM β-mercaptoethanol).

    Affinity Purification:

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: This procedure introduces a 6xHis tag to the N-terminus of the fusion proteins to allow affinity purification. .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions.

    Recombinant:

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. Recombinant His-MBD protein was purified from inclusion bodies of 500 ml BL21-AI cells 24 hours after induction with 0.2% L-arabinose.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The digested plasmid and PCR product containing full-length recombinant A. gambiae β-CA gene were purified and then ligated overnight at +4 °C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: Paragraph title: Construction of recombinant baculoviruses ... The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Cellular Antioxidant Activity Assay:

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Combined Bisulfite Restriction Analysis Assay:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Paragraph title: Bisulfite-sequencing and combined bisulfite-restriction analysis (COBRA) ... Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Methylation:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The methylation pattern in DMRs was analyzed using CpGviewer software.

    Mutagenesis:

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: Paragraph title: Sirt2 KO mutation sequencing ... The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions.

    Isolation:

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: Total RNA isolated using the Pico Pure RNA isolation kit (Arcturus) was converted to cDNA using pd(N)6 primer (Pharmacia Biotech) and standard procedures. .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems).

    Size-exclusion Chromatography:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Both first and second round PCR were performed at 2 cycles of 2 min at 95°C, 1 min at 55°C, 1 min at 72°C, and subsequent 35 cycles of 30 sec at 95°C, 1 min at 55°C, 1 min at 72°C, and 1 cycle of 10 min at 72°C. .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Purification:

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. Recombinant His-MBD protein was purified from inclusion bodies of 500 ml BL21-AI cells 24 hours after induction with 0.2% L-arabinose.

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions. .. The purified proteins were concentrated with Amicon Ultra-15 centrifugal filters (MWCO 10,000, Millipore, MA), dialyzed against 100mM sodium phosphate buffer, pH 7.4 and stored at 4°C.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The digested plasmid and PCR product containing full-length recombinant A. gambiae β-CA gene were purified and then ligated overnight at +4 °C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. To proceed with the fusion of eGFP sequences to their vectors (pApo, pIFN and pIA respectively), both plasmids were digested with the appropriate enzymes (New England Biolabs, UK) for each case.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The digested plasmid and DmBCA-GFP construct were purified and then ligated overnight at +4°C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: LM-PCR products were gel purified (QIAGEN) and ligated into the pCR2.1TOPO vector (Invitrogen) following the manufacturer's directions. .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer.

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Protein Purification:

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: Paragraph title: Fluorescent protein purification ... Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Germinal centers in human lymph nodes contain reactivated memory B cells
    Article Snippet: .. VH1/VH4-IgVH RT-PCR products were cloned into pTOPO-TA vectors and transformed into TOP10 bacteria (Invitrogen) to generate molecular IgVH clones. .. Sequencing on both strands was performed using the big dye terminator cycle sequencing kit (Applied Biosystems).

    Article Title: Among B cell non-Hodgkin's lymphomas, MALT lymphomas express a unique antibody repertoire with frequent rheumatoid factor reactivity
    Article Snippet: .. Cloning and sequencing IgV RT-PCR products of MALT lymphomas were either directly sequenced or cloned into pTOPO-TA-vectors and transformed into TOP10 bacteria (Invitrogen), to generate molecular IgV clones. .. Sequencing on both strands was performed by an ABI sequencer (Applied Biosystems) using the big dye-terminator cycle-sequencing kit.

    Article Title: CD20 deficiency in humans results in impaired T cell-independent antibody responses
    Article Snippet: .. IgM-VH3 and IgG-VH3 RT-PCR products were cloned into pTOPO-TA vectors, transformed into TOP10 bacteria (Invitrogen), and sequenced on both strands using the BigDye Terminator Cycle Sequencing Kit (Applied Biosystems). .. To determine the germline genes used in the IgVH -DH -JH rearrangements, the somatic IgVH mutations therein, and the IgVH -CDR3 amino acid sequence lengths, the sequences were compared with published germline IgVH genes using the Vbase database ( ) and DNAplot online (MRC Centre for Protein Engineering; ).

    Confocal Microscopy:

    Article Title: Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa
    Article Snippet: In addition to luciferase expression, in a subset of clones’ green fluorescent protein (GFP) expression was also captured using confocal microscopy (Olympus Fluoview v2.0b). .. The ligated mixture was transformed into TOP10 bacteria (Life Technologies) and inoculated directly in the LB broth supplemented with ampicillin to retain the viral diversity.

    Nested PCR:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: DMRs of imprinted-genes were amplified by nested PCR using bisulfite treated gDNA and specific primers ( ). .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Activated Clotting Time Assay:

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Mouse Assay:

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: Sirt2 KO mutation sequencing Tail-tip DNA from Sirt2 KO mice and WT littermates was used for PCR with Qiagen Type-it Mutation Detection kit using 200 ng DNA in a 50 µL reaction containing 25 µL 2× Master mix, 5 µL Sirt2 forward primer, 5 µL Sirt2 reverse KO primer and 10 µL Q solution, with cycling conditions of: 95°C for 10 min, (95°C for 30 s, 65°C for 90 s, 72°C for 60 s)×30 and 68°C for 10 min. .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions.

    Plasmid Preparation:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The plasmids were prepared using a QIAprep Spin Miniprep Kit (Qiagen Inc) and sequenced with M13 forward and reverse primers.

    Article Title: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
    Article Snippet: .. The PCR fragment was cloned into pENTR/D-TOPO plasmid and propagated in TOP10 bacteria (Invitrogen). .. The insert was fully sequenced and then recombined into the pDEST-17 bacterial expression vector using the Gateway system (Invitrogen).

    Article Title: Single action potentials and subthreshold electrical events imaged in neurons with a novel fluorescent protein voltage probe
    Article Snippet: Expression constructs were generated by inserting PCR-amplified fragments of super ecliptic pHluorin or super ecliptic pHluorin A227D cDNA into the pCR4Blunt TOPO vector (Invitrogen, NY). .. Top10 bacteria (Invitrogen, NY) were transformed with the expression constructs and fusion proteins were purified with His-Select™ Nickel Affinity Gel (Sigma-Aldrich, MO), following the manufacturer’s instructions.

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The digested plasmid and PCR product containing full-length recombinant A. gambiae β-CA gene were purified and then ligated overnight at +4 °C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: IFNα plasmid (pIFN), ApoAI plasmid (pApoAI) and IFNα bound to ApoAI plasmid (pIFNApoAI) had been previously synthesized in the laboratory . .. The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification.

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The digested plasmid and DmBCA-GFP construct were purified and then ligated overnight at +4°C using T4 DNA ligase (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. ..

    Article Title: Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development
    Article Snippet: .. Reporter constructs Highly conserved sequence elements from GLI3 introns (CNE1, 6, 9, 10, 11) (Figure ) were chosen as candidate enhancer sequences and PCR amplified using a high-fidelity DNA polymerase (Herculase® , Stratagene) with primers containing restriction site tags [ , ], inserted into the p1230 vector (a generous gift of R. Krumlauf) in front of the human β-globin minimal promoter driving a lacZ reporter gene [ ], and cloned in Top10 bacteria (Invitrogen) using standard technology. .. Purified plasmids were controlled for correctness of insert sequences by automated sequencing (ABI 377, Applied Biosystems).

    Software:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen). .. The methylation pattern in DMRs was analyzed using CpGviewer software.

    Selection:

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: .. TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. ..

    Agarose Gel Electrophoresis:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: After agarose gel electrophoresis, amplicons were eluted using QIAquick Gel Extraction Kits (Qiagen Inc). .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Article Title: Anion inhibition studies of a beta carbonic anhydrase from the malaria mosquito Anopheles gambiae
    Article Snippet: The PCR product was run on an agarose gel, and the obtained band was purified. pFastBacTM 1 plasmid (Invitrogen, Carlsbad, CA) and the PCR product were digested at +37 °C overnight with BamHI and XhoI restriction enzymes (New England Biolabs, Ipswich, MA). .. The ligated product was transformed into TOP10 bacteria (Invitrogen, Helsinki, Finland).

    Article Title: Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates
    Article Snippet: The PCR product was run on an agarose gel, and the obtained band was purified. pFastBac™ 1 plasmid (Invitrogen) and the PCR product were digested at +37°C overnight with BamHI and XhoI restriction enzymes (New England Biolabs). .. The ligated product was transformed into TOP10 bacteria (Invitrogen).

    Laser Capture Microdissection:

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: Dilution steps ranging from 100 ng to 1 pg DNA were amplified with primer Lam-5 (5′-tag agc gat tta tct tct gaa c-3′) and Lam-3 (5′-cgg cgc ata gct gat aac-3′) as described above except for the following modifications: the total number of cycles was 25 and the annealing temperature was 55°C. .. TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ).

    Concentration Assay:

    Article Title: Kinetic and Dynamic Computational Model-Based Characterization of New Proteins in Mice: Application to Interferon Alpha Linked to Apolipoprotein A-I
    Article Snippet: The resulting products were purified (Qiagen, Madrid, Spain), cloned into pcDNA™3.1/V5-His TOPO® TA expression vectors, according to the instructions provided by the manufacturer, and transformed into Top10 bacteria (Invitrogen, CA, USA) for amplification. .. Afterwards, the open plasmids and their purified inserts were fused using T4 DNA ligase High Concentration and 2X Rapid Ligation Buffer (Promega, Madison, WI, USA).

    Alkaline Lysis:

    Article Title: Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling
    Article Snippet: TOP10 bacteria (Invitrogen) were transformed with the pCR2.1TOPO plasmid carrying LM-PCR inserts and streaked onto LB-agar plates supplemented with ampicillin (50 μg/ml) for blue/white colony selection as directed by the manufacturer. .. Cloned plasmid inserts were then purified by alkaline lysis extraction (QIAGEN) and sequenced with the M13 reverse primer by the Duke University DNA Sequencing Facility.

    CTG Assay:

    Article Title: Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)
    Article Snippet: TOP10 bacteria were transformed with the ligation products as recommended by the manufacturers (Invitrogen, Groningen, The Netherlands) and bacteria from blue/white-selected single colonies were transferred into 100 µl reaction mixtures containing 1× AmpliTaq PCR buffer II, 2 mM MgCl2 , 30 pmol F-primer (5′-agg cga tta agt tgg gta ac-3′), 30 pmol R-primer (5′-cag cta tga cca tga tta cg-3′), 200 µM of each dNTP and 1 U Ampli Taq ). .. The Genetics Computer Group (GCG, Madison, WI) program package, version 10.0 was used to design pairs of primer specific for the following sequences: TSC-22R (I: 5′-tag aca aca aga tcg aac ag-3′; II: 5′-tgt gct agg tgt aaa gtt ctc-3′), TSPY (I: 5′-gaa gaa tcg tcc att tcc aga atc-3′; II: 5′-aag tct gat ggg gca aca gc-3′), TAP2 (I: 5′-ggt gaa caa caa agt ctt gat gtg-3′; II: 5′-tgt ctt agt ctc ctg gaa gaa ac-3′), HLA-DQA (I: 5′-gag gaa gga gac tgt ctg g-3′; II: 5′-agg gag gaa ggt gag gta ac-3′), HLA-DRB (I: 5′-tga tgc tgg aaa cag ttc ctc-3′; II: 5′-gtc atc tgc act tca gct c-3′), HLA-DRA (I: 5′-tcc cag aga cta cag aga ac-3′; II: 5′-ctc tct aag aaa cac cat cac-3′) and Notch4 (I: 5′-ctg tga gga gaa cct gga tg-3′; II: 5′-tga cac agg cag agt gtg g-3′).

    Gel Extraction:

    Article Title: Novel Epigeneitc Mechanisms that Control Pluripotency and Quiescence of Adult Bone Marrow-Derived Oct4+ Very Small Embryonic Like Stem Cells
    Article Snippet: After agarose gel electrophoresis, amplicons were eluted using QIAquick Gel Extraction Kits (Qiagen Inc). .. Eluted amplicons were subsequently ligated into pCR® 2.1-TOPO® vector and transformed into TOP10 bacteria using a TOPO TA Cloning Kit (Invitrogen).

    Article Title: SIRT2 Ablation Has No Effect on Tubulin Acetylation in Brain, Cholesterol Biosynthesis or the Progression of Huntington's Disease Phenotypes In Vivo
    Article Snippet: .. The PCR product was purified with the Qiaquick Gel Extraction kit according to manufacturer's instructions and cloned into TOP10 bacteria using the Invitrogen TOPO TA cloning kit according to manufacturer's instructions. .. Plasmid DNA was isolated with Qiaprep Spin Miniprep Kit according to manufacturer's instructions and eluted in ultra-pure water.

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