PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli.

PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli.

We just lately demonstrated that the Escherichia coli ribosome is strong sufficient to accommodate international 16S rRNAs from numerous gamma- and betaproteobacteria micro organism (Kitahara et al., 2012).

Therein, we used the widespread common primers Bac8f and UN1541r to acquire a virtually full-length gene. Nevertheless, we observed that these primers overlap variable websites at 19[A/C] and 1527[U/C] in Bac8f and UN1541r, respectively, and thus, the amplicon might include mutations.

That is problematic, notably for the previous website, as a result of the 19th nucleotide pairs with the 916th nucleotide, which is part of the “central pseudoknot” and is important for perform. Due to this fact, we mutationally investigated the function of the bottom pair utilizing a number of 16S rRNAs from gamma- and betaproteobacteria.

We discovered that each the native base pairs (gammaproteobacterial 19A-916U and betaproteobacterial 19C-916G) and the non-native 19A-916G pair retained perform, whereas the non-native 19C-916U was faulty 16S rRNAs. We subsequent designed a brand new primer set, Bac1f and UN1542r, in order that they don’t overlap the potential mismatch websites. 16S rRNA amplicons obtained from the environmental metagenome utilizing the brand new primer set had been dominated by proteobacterial species (~85%).

Subsequent purposeful screening recognized varied 16S rRNAs from proteobacteria, all of which contained native 19A-916U or 19C-916G base pairs. The primers developed on this examine are thus advantageous for purposeful characterization of international 16S rRNA in E. coli with no artifacts.

STITCHER 2.0: primer design for overlapping PCR purposes.

Overlapping polymerase chain response (PCR) is a standard method utilized by researchers in very numerous fields that allows the consumer to ‘sew’ particular person items of DNA collectively. Beforehand, we have now reported an online primarily based device referred to as STITCHER that gives a platform for researchers to automate the design of primers for overlapping PCR purposes.

Right here we current STITCHER 2.0, which represents a considerable replace to STITCHER. STITCHER 2.Zero is a newly designed net device that automates the design of primers for overlapping PCR. In contrast to STITCHER, STITCHER 2.Zero considers numerous algorithmic parameters, and returns a number of end result information that embrace a facility for the consumer to attract their very own primers in addition to complete visible guides to the consumer’s enter, output, and designed primers. These end result information present better management and perception throughout experimental design and troubleshooting.

PrimerSuite: A Excessive-Throughput Net-Based mostly Primer Design Program for Multiplex Bisulfite PCR.

The evaluation of DNA methylation at CpG dinucleotides has turn into a significant analysis focus on account of its regulatory function in quite a few organic processes, however the requisite want for assays which amplify bisulfite-converted DNA represents a significant bottleneck as a result of distinctive design constraints imposed on bisulfite-PCR primers.

PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli.

Furthermore, a overview of the literature indicated no out there software program options which accommodated each high-throughput primer design, help for multiplex amplification assays, and primer-dimer prediction. In response, the tri-modular software program package deal PrimerSuite was developed to help bisulfite multiplex PCR purposes.

This software program was constructed to (i) design bisulfite primers towards a number of areas concurrently (PrimerSuite), (ii) display screen for primer-primer dimerizing artefacts (PrimerDimer), and (iii) help multiplex PCR assays (PrimerPlex). Furthermore, a significant focus within the growth of this software program package deal was the emphasis on intensive empirical validation, and over 1300 distinctive primer pairs have been efficiently designed and screened, with over 94% of them producing amplicons of the anticipated measurement, and a mean mapping effectivity of 93% when screened utilizing bisulfite multiplex resequencing. The potential use of the software program in different bisulfite-based purposes akin to methylation-specific PCR is into consideration for future updates.

PrimerMapper: excessive throughput primer design and graphical meeting for PCR and SNP detection.

Primer design represents a extensively employed gambit in numerous molecular purposes together with PCR, sequencing, and probe hybridization. Variations of PCR, together with primer strolling, allele-specific PCR, and nested PCR present specialised validation and detection protocols for molecular analyses that always require screening giant numbers of DNA fragments.

In these instances, automated sequence retrieval and processing turn into vital options, and moreover, a graphic that gives the consumer with a visible information to the distribution of designed primers throughout targets is most useful in rapidly ascertaining primer protection. To this finish, I describe right here, PrimerMapper, which supplies a complete graphical consumer interface that designs strong primers from any variety of inputted sequences whereas offering the consumer with each, graphical maps of primer distribution for every inputted sequence, and likewise a world assembled map of all inputted sequences with designed primers.

PrimerMapper additionally allows the visualization of graphical maps inside a browser and permits the consumer to attract new primers immediately onto the webpage.

Pro QPCR SuperMix Kit

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Pro QPCR SuperMix Kit - ROX premixed

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Green qPCR SuperMix UDG

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Green qPCR SuperMix UDG

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Top Green qPCR SuperMix

abx098033-100l 100 µl
EUR 262.5

Top Green qPCR SuperMix

abx098033-200l 200 µl
EUR 487.5

Tip Green qPCR SuperMix

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EUR 262.5

Tip Green qPCR SuperMix

abx098034-200l 200 µl
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Fast Pro QPCR SuperMix Kit - ROX premixed

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Library Quantification qPCR SuperMix

abx098896-100l 100 µl
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Tip Green qPCR SuperMix (+Dye II)

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Tip Green qPCR SuperMix (+Dye II)

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cDNA Synthesis SuperMix for qPCR

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HyperScript RT SuperMix for qPCR

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EUR 280
Description: High efficiency reverse transcription reaction premixed solution for two-step RT-qPCR method

HyperScript RT SuperMix for qPCR

K1074-50 50 rxn (20 uL/rxn)
EUR 150
Description: High efficiency reverse transcription reaction premixed solution for two-step RT-qPCR method

cDNA Synthesis SuperMix for qPCR

abx098019-100l 100 µl
EUR 825

cDNA Synthesis SuperMix for qPCR

abx098019-1ml 1 ml
EUR 2387.5

cDNA Synthesis SuperMix for qPCR

abx098019-200l 200 µl
EUR 1000

HiScript II Q RT SuperMix for qPCR

R222-01 100 rxn (20 μl/rxn)
EUR 145

EnTurbo™ SYBR Color qPCR SuperMix (Without ROX)

EQ035 5mL
EUR 340

cDNA Synthesis SuperMix for qPCR (GC-rich)

abx098024-50rxns20ulSystems 50 rxns × 20 ul Systems
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cDNA Synthesis SuperMix for qPCR (GC-rich)

abx098024-100l 100 µl
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cDNA Synthesis SuperMix for qPCR (GC-rich)

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HiScript II Q Select RT SuperMix for qPCR

R232-01 100 rxn (20 μl/rxn)
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HiScript IV RT SuperMix for qPCR (+gDNA wiper)

R423-01 100rxns(20µl/rxn)
EUR 326

HiScript III RT SuperMix for qPCR (+gDNA wiper)

R323-01 100 rxn (20 μl/rxn)
EUR 217.5

Uni Cell to cDNA Synthesis SuperMix for qPCR

abx098860-100l 100 µl
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Uni Cell to cDNA Synthesis SuperMix for qPCR

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Uni Cell to cDNA Synthesis SuperMix for qPCR

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EnTurbo™ SYBR Color qPCR SuperMix (Low ROX Premixed)

EQ033 5mL
EUR 340

EnTurbo™ SYBR Color qPCR SuperMix (High ROX Premixed)

EQ034 5mL
EUR 340

HyperScript RT SuperMix for qPCR (with gDNA wiper)

K1174-100 100 rxns
EUR 304
Description: High efficiency reverse transcription reaction premixed solution for two-step RT-qPCR method

HyperScript RT SuperMix for qPCR (with gDNA wiper)

K1174-50 50 rxns
EUR 176
Description: High efficiency reverse transcription reaction premixed solution for two-step RT-qPCR method

HiScript II Q RT SuperMix for qPCR (+gDNA wiper)

R223-01 100rxns(20µl/rxn)
EUR 159.5

QCell-Eva One-Step qRT-PCR SuperMix Kit

K5054200 200 reactions
EUR 468

QCell-Eva One-Step qRT-PCR SuperMix Kit

K5054400 400 reactions
EUR 711

HiScript II Q Select RT SuperMix for qPCR (+gDNA wiper)

R233-01 100 rxn (20 μl/rxn)
EUR 159.5

Fast QCell-Eva One-Step qRT-PCR SuperMix Kit

K5054002 200 rxn
EUR 468

Fast QCell-Eva One-Step qRT-PCR SuperMix Kit

K5054004 400 rxn
EUR 711

HiScript III All-in-one RT SuperMix Perfect for qPCR

R333-01 100 rxns (21 μl/rxn)
EUR 217.5

PCR SuperMix

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MB200-P100 100 rxns2 x 1.25 mL
EUR 11

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20-abx098002
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PCR SuperMix (-dye)

abx098002-100l 100 µl
EUR 237.5

PCR SuperMix (-dye)

abx098002-200l 200 µl
EUR 337.5

PCR SuperMix (+dye)

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EUR 237.5

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EUR 337.5

Plus PCR SuperMix

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Evo? cDNA Supermix

M1168-100 each
EUR 457.2

Evo? cDNA Supermix

M1168-25 each
EUR 320.4

Plus PCR SuperMix

abx098888-100l 100 µl
EUR 300

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abx098888-200l 200 µl
EUR 612.5

Novo? cDNA Supermix

M1169-100 each
EUR 529.2

Novo? cDNA Supermix

M1169-25 each
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Probe Direct SuperMix

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abx461057-596tests 5 × 96 tests
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T PCR SuperMix (-dye)

20-abx098005
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T PCR SuperMix (-dye)

abx098005-100l 100 µl
EUR 262.5

T PCR SuperMix (-dye)

abx098005-200l 200 µl
EUR 462.5

T PCR SuperMix (+dye)

abx098006-100l 100 µl
EUR 262.5

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abx098006-200l 200 µl
EUR 462.5

cDNA Synthesis SuperMix

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abx098014-100l 100 µl
EUR 725

cDNA Synthesis SuperMix

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cDNA Synthesis SuperMix

abx098014-200l 200 µl
EUR 812.5

AmpHS 2X PCR SuperMix

MB203-P100 100 rxns2 x 1.25 mL
EUR 11

QCell-Pro One-Step qRT-PCR SuperMix Kit

K5055200 200 reactions
EUR 427

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K5055400 400 reactions
EUR 682

EasyPfu PCR SuperMix (-dye)

20-abx098009
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20-abx098010
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FastPfu PCR SuperMix (-dye)

abx098010-100l 100 µl
EUR 300

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abx098010-200l 200 µl
EUR 575

Library Amplification SuperMix

20-abx098894
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Library Amplification SuperMix

abx098894-100l 100 µl
EUR 737.5

Library Amplification SuperMix

abx098894-200l 200 µl
EUR 1137.5

OneScriptcDNA Synthesis SuperMix

G451 25 x 20 ul reactions
EUR 106.8

OneScriptcDNA Synthesis SuperMix

G452 100 x 20 ul reactions
EUR 169.2

PCR SuperMix for PAGE (+dye)

20-abx098004
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PCR SuperMix for PAGE (+dye)

abx098004-100l 100 µl
EUR 237.5

PCR SuperMix for PAGE (+dye)

abx098004-200l 200 µl
EUR 337.5

Fast QCell-Pro One-Step qRT-PCR SuperMix Kit

K5055002 200 rxn
EUR 426

Fast QCell-Pro One-Step qRT-PCR SuperMix Kit

K5055004 400 rxn
EUR 682

OneScriptPlus cDNA Synthesis SuperMix

G453 25 x 20 ul reactions
EUR 116.4

OneScriptPlus cDNA Synthesis SuperMix

G454 100 x 20 ul reactions
EUR 202.8

OmniPCR Supermix w Fluorescent dye

MBA01-0100 100 rxns (2.5ml)
EUR 16

EnTurbo™ SYBR Green PCR SuperMix

EQ001 5mL
EUR 340

AmpLong 2X PCR SuperMix (15-30 sec/kb; ≤20kb, 1X)

MB204-P100 100 rxns2 x 1.25 mL
EUR 13

Green Two-Step qRT-PCR SuperMix

abx098035-50rxns20ulRTSystems300rxns20ulqPCRSystems 50 rxns × 20 ul (RTSystems) / 300 rxns × 20 ul (qPCRSystems)
EUR 777.6

Green One-Step qRT-PCR SuperMix

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Green Two-Step qRT-PCR SuperMix

abx098035-100l 100 µl
EUR 925

Green Two-Step qRT-PCR SuperMix

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Green Two-Step qRT-PCR SuperMix

abx098035-200l 200 µl Ask for price

Green One-Step qRT-PCR SuperMix

abx098038-100l 100 µl
EUR 737.5

Green One-Step qRT-PCR SuperMix

abx098038-1ml 1 ml Ask for price

Green One-Step qRT-PCR SuperMix

abx098038-200l 200 µl
EUR 1050

Probe One-Step qRT-PCR SuperMix

abx098042-100l 100 µl
EUR 850

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abx098042-200l 200 µl
EUR 1400

Two-Step RT-PCR SuperMix (12 kb)

abx098025-50rxns20ulRTSystems80rxns50ulPCRSystems 50 rxns × 20 ul (RT Systems) / 80 rxns × 50 ul (PCR Systems)
EUR 727.2

Two-Step RT-PCR SuperMix (15 kb)

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EUR 910.8

Two-Step RT-PCR SuperMix (12 kb)

abx098025-100l 100 µl
EUR 887.5

Two-Step RT-PCR SuperMix (12 kb)

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abx098025-200l 200 µl Ask for price

Two-Step RT-PCR SuperMix (15 kb)

abx098026-100l 100 µl
EUR 1087.5

Two-Step RT-PCR SuperMix (15 kb)

abx098026-1ml 1 ml Ask for price

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AmpFAST 2X PCR SuperMix (5-30 sec/kb; ≤6kb, 1X)

MB202-P100 100 rxns2 x 1.25 mL
EUR 11

All-in-One cDNA Synthesis SuperMix

B24403 200 ractions
EUR 547.2
Description: All-in-One cDNA Synthesis SuperMix contains all the necessary components pre-blended in one tube for reverse transcription.

All-in-One cDNA Synthesis SuperMix

B24408 1000 ractions
EUR 1743.6
Description: All-in-One cDNA Synthesis SuperMix contains all the necessary components pre-blended in one tube for reverse transcription.

OmniPCR HS Supermix w Fluorescent dye

MBA03-0100 100 rxns2 x 1.25 mL
EUR 16

OmniPCR FAST Supermix w Fluorescent dye

MBA02-0100 100 rxns2 x 1.25 mL
EUR 16

OmniPCR Long Supermix w Fluorescent dye

MBA04-0100 100 rxns2 x 1.25 mL
EUR 16

One-Step RT-PCR SuperMix (+dye) (4 kb)

abx098027-200rxns20ulSystems 200 rxns × 20 ul Systems
EUR 727.2

One-Step RT-PCR SuperMix (+dye) (8 kb)

abx098028-200rxns20ulSystems 200 rxns × 20 ul Systems
EUR 794.4

One-Step RT-PCR SuperMix (+dye) (8 kb)

abx098029-200rxns20ulSystems 200 rxns × 20 ul Systems
EUR 1028.4

One-Step RT-PCR SuperMix (+dye) (4 kb)

abx098027-100l 100 µl
EUR 875

One-Step RT-PCR SuperMix (+dye) (4 kb)

abx098027-1ml 1 ml Ask for price

One-Step RT-PCR SuperMix (+dye) (4 kb)

abx098027-200l 200 µl Ask for price

One-Step RT-PCR SuperMix (+dye) (8 kb)

abx098028-100l 100 µl
EUR 950

One-Step RT-PCR SuperMix (+dye) (8 kb)

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One-Step RT-PCR SuperMix (+dye) (8 kb)

abx098028-200l 200 µl Ask for price

One-Step RT-PCR SuperMix (+dye) (8 kb)

abx098029-100l 100 µl
EUR 1212.5

One-Step RT-PCR SuperMix (+dye) (8 kb)

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One-Step RT-PCR SuperMix (+dye) (8 kb)

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Fly First-Strand cDNA Synthesis SuperMix

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Fly First-Strand cDNA Synthesis SuperMix

abx098858-100l 100 µl
EUR 850

Fly First-Strand cDNA Synthesis SuperMix

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Fly First-Strand cDNA Synthesis SuperMix

abx098858-200l 200 µl
EUR 1037.5

Green miRNA Two-Step qRT-PCR SuperMix

abx098036-20rxns20ulRTSystems500rxns20ulqPCRSystems 20 rxns × 20 ul (RTSystems) / 500 rxns × 20 ul (qPCRSystems)
EUR 1062

Green miRNA Two-Step qRT-PCR SuperMix

abx098036-100l 100 µl
EUR 1212.5

Green miRNA Two-Step qRT-PCR SuperMix

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Green miRNA Two-Step qRT-PCR SuperMix

abx098036-200l 200 µl Ask for price

miRNA First-Strand cDNA Synthesis SuperMix

abx098020-20rxns20ulSystems 20 rxns × 20 ul Systems
EUR 878.4

miRNA First-Strand cDNA Synthesis SuperMix

abx098020-100l 100 µl
EUR 950

miRNA First-Strand cDNA Synthesis SuperMix

abx098020-1ml 1 ml Ask for price

miRNA First-Strand cDNA Synthesis SuperMix

abx098020-200l 200 µl Ask for price

High Fidelity (HiFi) PCR SuperMix (-dye) (DNA, PCR)

20-abx098007
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Green Two-Step qRT-PCR SuperMix (GC Rich)

abx098037-50rxns20ulRTSystems300rxns20ulqPCRSystems 50 rxns × 20 ul (RTSystems) / 300 rxns × 20 ul (qPCRSystems)
EUR 961.2

Green One-Step qRT-PCR SuperMix (GC Rich)

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Probe One-Step qRT-PCR SuperMix (GC Rich)

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High Fidelity (HiFi) PCR SuperMix (-dye) (DNA, PCR)

abx098007-100l 100 µl
EUR 262.5

High Fidelity (HiFi) PCR SuperMix (-dye) (DNA, PCR)

abx098007-200l 200 µl
EUR 475

Green Two-Step qRT-PCR SuperMix (GC Rich)

abx098037-100l 100 µl
EUR 1125

Green Two-Step qRT-PCR SuperMix (GC Rich)

abx098037-1ml 1 ml Ask for price

Green Two-Step qRT-PCR SuperMix (GC Rich)

abx098037-200l 200 µl Ask for price

Green One-Step qRT-PCR SuperMix (GC Rich)

abx098039-100l 100 µl
EUR 450

Green One-Step qRT-PCR SuperMix (GC Rich)

abx098039-1ml 1 ml Ask for price

Green One-Step qRT-PCR SuperMix (GC Rich)

abx098039-200l 200 µl
EUR 1000

Probe One-Step qRT-PCR SuperMix (GC Rich)

abx098041-100l 100 µl
EUR 737.5

Probe One-Step qRT-PCR SuperMix (GC Rich)

abx098041-1ml 1 ml Ask for price

Probe One-Step qRT-PCR SuperMix (GC Rich)

abx098041-200l 200 µl
EUR 1050

First-Strand cDNA Synthesis SuperMix for PCR

abx098018-50rxns20ulSystems 50 rxns × 20 ul Systems
EUR 693.6

First-Strand cDNA Synthesis SuperMix for PCR

abx098018-100l 100 µl
EUR 850

First-Strand cDNA Synthesis SuperMix for PCR

abx098018-1ml 1 ml Ask for price

First-Strand cDNA Synthesis SuperMix for PCR

abx098018-200l 200 µl Ask for price

HyperScript First-Strand cDNA Synthesis SuperMix

K1073-100 100 rxn (20 uL/rxn)
EUR 282
Description: Reverse transcription reaction premixed solution for efficient synthesis of first-strand cDNA.

HyperScript First-Strand cDNA Synthesis SuperMix

K1073-50 50 rxn (20 uL/rxn)
EUR 150
Description: Reverse transcription reaction premixed solution for efficient synthesis of first-strand cDNA.

One-Step gDNA Removal and cDNA Synthesis SuperMix

20-abx09885920ulSystems
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One-Step gDNA Removal and cDNA Synthesis SuperMix

abx098859-100l 100 µl
EUR 1062.5

One-Step gDNA Removal and cDNA Synthesis SuperMix

abx098859-1ml 1 ml Ask for price

One-Step gDNA Removal and cDNA Synthesis SuperMix

abx098859-200l 200 µl
EUR 1425

EnTurbo™ SYBR Green PCR SuperMix(Low ROX Premixed)

EQ014 5mL
EUR 340

EnTurbo™ SYBR Green PCR SuperMix(High ROX Premixed)

EQ013 5mL
EUR 340

First-Strand cDNA Synthesis SuperMix (cDNA up to 12 kb)

20-abx09801620ulSystems
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  • 100 rxns × 20 ul Systems
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First-Strand cDNA Synthesis SuperMix (cDNA up to 15 kb)

20-abx09802120ulSystems
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  • 100 rxns × 20 ul Systems
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First-Strand cDNA Synthesis SuperMix (cDNA up to 12 kb)

abx098016-100l 100 µl
EUR 775

First-Strand cDNA Synthesis SuperMix (cDNA up to 12 kb)

abx098016-1ml 1 ml Ask for price

First-Strand cDNA Synthesis SuperMix (cDNA up to 12 kb)

abx098016-200l 200 µl
EUR 912.5

First-Strand cDNA Synthesis SuperMix (cDNA up to 15 kb)

abx098021-100l 100 µl
EUR 962.5

First-Strand cDNA Synthesis SuperMix (cDNA up to 15 kb)

abx098021-1ml 1 ml Ask for price

First-Strand cDNA Synthesis SuperMix (cDNA up to 15 kb)

abx098021-200l 200 µl
EUR 1237.5

One-Step gDNA Removal and cDNA Synthesis SuperMix (15kb)

20-abx09802220ulSystems
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  • Ask for price
  • 100 rxns × 20 ul Systems
  • 50 rxns × 20 ul Systems

One-Step gDNA Removal and cDNA Synthesis SuperMix (15kb)

abx098022-100l 100 µl
EUR 1012.5

One-Step gDNA Removal and cDNA Synthesis SuperMix (15kb)

abx098022-1ml 1 ml Ask for price

One-Step gDNA Removal and cDNA Synthesis SuperMix (15kb)

abx098022-200l 200 µl
EUR 1325

One-Step gDNA Removal and cDNA Synthesis SuperMix (8 kb)

20-abx09801520ulSystems
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  • Ask for price
  • 100 rxns × 20 ul Systems
  • 50 rxns × 20 ul Systems

One-Step gDNA Removal and cDNA Synthesis SuperMix (12 kb)

20-abx09801720ulSystems
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  • Ask for price
  • 100 rxns × 20 ul Systems
  • 50 rxns × 20 ul Systems

Different options of PrimerMapper embrace allele-specific design options for SNP genotyping, a distant BLAST window to NCBI databases, and distant sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely out there with out restriction.

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