Webinar: Tips for effective use of BLAST and other NCBI tools

August 17, 2016 by · Leave a Comment 

BLAST Screenshot

This looks like being a very useful webinar for researchers working across a whole range of molecular biology disciplines. Everyone “kinda knows” how to use BLAST, but there are always tools and capabilities hidden in such resources that we don’t know (“known unknowns,” you might say).

The tools are indispensable when planning genomics experiments, including for qPCR, NGS, and CRISPR. In this presentation, Dr Matt McNeill, from Integrated DNA Technologies (IDT), will take a practical look at getting started with the wealth of NCBI tools, and share some relevant tips to help you sift through the tools and options that IDT regularly use. In particular, he will focus on commonly adjusted parameters that will allow you to more effectively use the powerful Basic Local Alignment Algorithm Tool (BLAST) to identify off-target hybridization/annealing events. Dr McNeill will cover practical examples using NCBI tools to design assays and, following the presentation, we will answer questions from attendees.

Date:

Tuesday, August 23, 2016

Time:

Session 1: 9:00 am CDT (UTC-5 hours)
Session 2: 1:00 pm CDT (UTC-5 hours)

24/06/16: Save Money and Protect the Environment…with Mastermix?!

June 24, 2016 by · Comments Off on 24/06/16: Save Money and Protect the Environment…with Mastermix?! 

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A nice article from IDT on their new qPCR Mastermix. It ships on ambient temperature, saving on dry ice, weighing less, costing less. Read on

13/05/16: From IDT – Finally, an Affordable CRISPR-Cas9 Endonuclease

May 13, 2016 by · Leave a Comment 

CRISPR_111615_560.jpg

A new one from Integrated DNA Technologies.

Improve the performance of your genome editing by combining Alt-R S.p. Cas9 Nuclease 3NLS with optimized Alt-R CRISPR crRNA and tracrRNA

  • Focus on results with higher potency CRISPR reagents
  • Save time and costs with efficient workflow and ready-to-use reagents
  • Increase precision and reduce off-target editing using CRISPR-Cas9 ribonucleoprotein
  • Adapt to your experimental needs with compatibility for lipofection or electroporation

Alt-R™ S.p Cas9 Nuclease 3NLS

The Alt-R S.p. Cas9 Nuclease 3NLS enzyme is a high purity, recombinant S. pyogenes Cas9. The enzyme includes 1 N-terminal nuclear localization sequence (NLS) and 2 C-terminal NLSs, as well as a C-terminal 6-His tag. The molecular weight of the nuclease is 163,700 g/mol. The S. pyogenes Cas9 enzyme must be combined with a crRNA and tracrRNA in order to produce a functional, target-specific editing complex. For the best editing, combine the Alt-R S.p. Cas9 Nuclease 3NLS enzyme with the optimized Alt-R CRISPR crRNA and tracrRNA in equimolar amounts.

Product specifications:

Alt-R™ S.p Cas9 Nuclease 3NLS

  • Amount provided: 100 µg or 500 µg
  • Molecular weight: 163,700 g/mol
  • Concentration: 10 µg/µL in 50% glycerol, [61 µM]
  • Endotoxin tested: <2 EU/mg
  • Shipping conditions: dry ice Store at –20°C

Dilute S.p Cas9 Nuclease to working concentration in 20 mM HEPES, 150 mM KCI, pH 7.5, or Opti-MEM® (Thermo Fisher) before use.

12/05/16: CRISPR Webinar – Ribonucleoprotein delivery optimization for improved genome editing

May 12, 2016 by · Leave a Comment 

On Wednesday May 18th 2016, Integrated DNA Technologies (IDT) are hosting a webinar titled: “Alt-R™ CRISPR-Cas9 System: Ribonucleoprotein delivery optimization for improved genome editing

Webinar Abstract:

Struggling with low editing efficiency or delivery problems? IDT has developed a simple and affordable CRISPR-Cas9 solution that outperforms other methods. In this webinar, we present the advantages of using a Cas9:tracrRNA:crRNA ribonucleoprotein (RNP) complex in genome editing experiments, and explain why it is the most efficient driver for genome editing compared to alternative methods, such as expression plasmids or the use of sgRNAs. We will also review RNP delivery using cationic lipids and electroporation, and provide tips for optimized transfection in your system.

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(You should also register if you are unable to make it, if you want access to the webinar recording)

05/04/16: Get on Target: How Individually Synthesized Capture Probes will Enrich Your NGS Experiments

April 5, 2016 by · Leave a Comment 

 

welcomeImageYou are most welcome to join our online webinar on April 13th at 11oo:

Get on Target: How Individually Synthesized Capture Probes will Enrich Your NGS Experiments

IDT’s NGS Application Specialist Europe, Dr. Jacques du Preez, will explain how IDT’s unique solution for Target Enrichment results in higher uniformity of coverage, improved on-target percentage and maximum flexibility. IDT’s xGen Lockdown® Probes® were recently defined as “best in class” by one of the world leaders in clinical diagnostics.

Agenda:

  • History of Sequencing
  • High Level NGS Workflow
  • NGS Library Prep and Sequencing
  • Sequencing Results
  • NGS Platforms
  • Target Enrichment
  • IDT Solutions for NGS – Library Prep and Target Enrichment
  •  xGen® Lockdown® Probe Advantages
  • Applications and Customer Feedback

 

Register Button

 

 

25/11/15: 30% off xGen® Exome Research Panel

November 25, 2015 by · Leave a Comment 

Exome Sequencing

Another great great offer from Integrated DNA Technologies.

Stretch your lab budget further with a discount on IDT’s xGen Exome Research Panel. This GMP compliant panel covers 19,396 genes and spans 39 Mb of the human genome.

  • Get consistent results with individually synthesized and quality controlled target capture probes
  • Obtain actionable data with deep, uniform coverage
  • Complete experiments quickly with our 4 hour hybridization

Use promo code NGS848 to save 30% on the xGen Exome Research Panel, subject to conditions.

19/11/15: 30% Off gBlocks Until December 15th 2015

November 19, 2015 by · Leave a Comment 

Another great offer from Integrated DNA Technologies (IDT). If you already know gBlocks, you’ll be pleased. If you don’t know them, take up this offer, try out gBlocks and then you’ll be pleased.

Details of the offer:

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16/11/15: Great Offer from IDT – 30% Off Selected PrimeTime® qPCR Products

November 16, 2015 by · Leave a Comment 

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A great offer from IDT:

Stretch your lab budget further with a discount on PrimeTime® qPCR Assays and selected custom qPCR probes.

Successfully multiplex with ZEN or TAO™ Double-Quenched Probes:

  • Lower background fluorescence
  • Increased endpoint signal
  • Reduced crosstalk

Get product shipment in 2–6 days. Use code PTQ388 to receive 30% off selected PrimeTime products.

Please note: offer ends December 15th 2015

Related articles

06/11/15: Knockdown of lncRNAs: exploring RNAi and antisense oligo methods

November 6, 2015 by · Leave a Comment 

lncRNA Knockout

 

There has been some interest in IDT’s lncRNA webinar from a few weeks back – here in Denmark, where I “operate.”

So, for those interested in lncRNAs – particularly with respect to their knockout – here is the full webinar again:

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The presentation and full slideset can also be viewed/downloaded here.

29/10/15: Webinar – Increase efficiency of genome editing with the Alt-R™ CRISPR-Cas9 System: Design and use

October 29, 2015 by · Leave a Comment 

Dr Garrett Rettig, Research Scientist, Integrated DNA Technologies

A heads up about an upcoming webinar from IDT:

“Increase efficiency of genome editing with the Alt-R™ CRISPR-Cas9 System: Design and use”

Date
Wednesday, November 4, 2015

Time
Session 1: 9:00–10:00 am CST (1500-1600 Danish time)
Session 2: 1:00–2:00 pm CST (1900-2000 Danish time)

You will learn about:

  • Designing your target sequences and ordering them as Alt-R CRISPR crRNAs
  • Components of the Alt-R CRISPR-Cas9 System
  • The experimental process, step by step
  • Challenges and potential pitfalls, as well as tips and guidance towards successful genome editing experiments

Register Button

 

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26/10/15: Improve the Performance of Your Existing Targeted Sequencing Panel

October 26, 2015 by · Leave a Comment 

Lockdown NGS targeted sequencingResearchers in the next generation sequencing (NGS) field have a lot of choices when it comes to where they buy their targeted sequencing panels from. In my experience there is no doubt that these panels will peform as advertised, but they often could do with a little tweaking, in order to move from “good” to “better.” For example, I’ve talked to researchers who have mentioned that sometimes coverage in certain regions of their target is not as good as in the rest of their panel. Sometimes, e.g., in the case of GC-rich regions, it is quite difficult for certain manufacturers to be able to make the appropriate probe.

This is where IDT’s method of manufacturing each capture probe “one by one” comes in. You can supplement an existing pool of array-synthesized baits, with IDT xGen® Lockdown® Probes to improve capture of high GC content and gap regions.

Find out how, here.

 

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21/10/15: Webinar About the Alt-R™ CRISPR-Cas9 System

October 21, 2015 by · Leave a Comment 

IDT are great at posting their webinars onto YouTube. So, if you missed their last one, or simply want to know more about IDT’s New Alt-R™ CRISPR-Cas9 System, then watch on…

YouTube Preview Image

My previous post explains a little more about the new system, as well as providing external links to IDT’s relevant webpages.

 

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21/10/15: IDT’s New Alt-R™ CRISPR-Cas9 System

October 21, 2015 by · Leave a Comment 

So, Integrated DNA Technologies (IDT) have been busy…

Their new Alt-R CRISPR-Cas9 System includes all of the core components you need for efficient genome editing. The  Alt-R CRISPR-Cas9 System has high potency due to optimized Alt-R CRISPR crRNA and Alt-R CRISPR tracrRNA designs that increase editing efficiency.

And of course, IDT quality RNA oligonucleotides give you more full-length product than competitors’.

So, what can you expect from this new system?

  • Improve on-target genome editing performance with our optimized, shorter design of CRISPR crRNA and tracrRNA oligos.
  • Achieve lower toxicity and no innate cellular response as compared to in vitro transcribed guide RNA alternatives.
  • Save time and resources by eliminating in vitro transcription and purification steps.

In another post, I have placed a recent webinar transmitted by IDT that explains this new method.

CRISPR_2-part-rna-illustration

Components of the Alt-R™ CRISPR-Cas9 System for directing Cas9 endonuclease to genomic targets. The crRNA:tracrRNA complex uses optimized Alt-R crRNA and tracrRNA sequences that hybridize and then form a complex with Cas9 endonuclease to guide targeted cleavage of genomic DNA. The cleavage site is specified by the protospacer element of crRNA (thick green bar). The crRNA protospacer element recognizes 19–20 nt on the opposite strand of the NGG PAM site (see Figure 2 for design guidance). The PAM site must be present immediately downstream of the target sequence for cleavage to occur. Research by IDT scientists has shown that the Alt-R CRISPR-Cas9 System provides the highest percentage of on-target genome editing when compared to competing designs, including both native S. pyogenes crRNA:tracrRNA and single fusion sgRNA triggers.

 

 

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20/10/15: New Product and Special Offers: PrimeTime® Gene Expression Master Mix

October 20, 2015 by · Leave a Comment 

PrimeTime MasterMix PromotionHooray! Integrated DNA Technologies have released their new qPCR mastermix! Actually, this is the first qPCR mastermix product from IDT.

Their PrimeTime® Gene Expression Master Mix is a 2X solution designed for use in two-step RT-qPCR. The headlines about this new product are:

  • Achieve high efficiency qPCR under fast or standard cycling conditions
  • Multiplex without loss of sensitivity
  • Obtain consistent results from overnight experiments by capitalizing on exceptional benchtop stability

Sorry SYBR® users, currently this mastermix is only for probe-based assays for now. However, this is a good opportunity to try out IDT’s excellent (and relatively inexpensive probe-based PrimeTime qPCR assays).

As part of the new product release, There are special offers available. See above.

 

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02/10/15: Designing sgRNAs for CRISPR/Cas9 experiments

October 2, 2015 by · Leave a Comment 

rp_welcomeImage-300x1991.pngIn this very useful article from Integrated DNA Technologies, learn how CRISPR crRNA and tracrRNA sequences can be combined into a single sgRNA for simplified use in CRISPR RNA-guided genome editing.

Use gBlocks Gene Fragments to design a double-stranded DNA fragment containing your desired promoter linked to your specific sgRNA sequence. The fragment can then be used in several ways

 

 

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29/09/15: CRISPR Webinar

September 29, 2015 by · Leave a Comment 

CRISPR webinar: New RNA tools for optimized CRISPR/Cas9 genome editing

Gene Editing CRISPR1600, October 7, 2015 (Denmark time)

Program overview

The CRISPR/Cas9 system has emerged as one of the leading tools for modifying the genomes of organisms ranging from E. coli to humans. In this webinar, we will discuss various methods for generating the crRNA and tracrRNA components that are required for guiding the Cas9 endonuclease to genomic targets. You will also learn how to optimize a new 2-part CRISPR RNA system from IDT that offers multiple benefits over other technologies.
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29/09/15: High throughput qPCR: tips for analysis across multiple plates

September 29, 2015 by · Leave a Comment 

If you missed the webinar from a few weeks ago, given by Mikael Kubista of TATAA Biocenter, here it is:

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28/09/15: Increase sensitivity and precision in your qPCR experiments

September 28, 2015 by · Leave a Comment 

ZEN™ and TAO™ Double-Quenched Probes improve qPCR data

A lot of researchers I speak to are unaware that Integrated DNA Technologies (IDT, www.idtdna.com) are able to sell probe-based qPCR assays, providing them fast, at a great price and allowing researchers to see the sequences of their primer:probe combinations. Even fewer are unaware that IDT has actually made some innovation to the standard quencher-dye configuration of qPCR probes.

In this article from DECODED, you can get a little bit more information about IDT’s ZEN™ and TAO™ double-quenched probes and why they can really help your experiments by improving your qPCR data.

18/09/15: Running Agarose and Polyacrylamide Gels

September 18, 2015 by · Leave a Comment 

We’ve all had to at some time or another

Do you reckon you could teach a newbie the most important tips for running gels, from the top of your head right now? Sure, you know how to run gels, but if you were teaching best practice, do you think you could do it?

Why not check your memory and lab knowledge by reading this article from Integrated DNA Technologies and seeing if you are still a gel-master.

Running Agarose and Polyacrylamide Gels – Good Practice

 

 

 

11/09/15: Easy Resuspension and Dilution of Oligos

September 11, 2015 by · Leave a Comment 

Oligo Resuspension CalculatorWhen I did my first degree (Biochemistry, University of Wales), we had one course devoted entirely to calculations. It was one of those courses that, if you did it well, could really make a difference to your final degree. The exam paper was open-ended, i.e., no fixed time limit, unlike most exams, which were limited to three hours. So, if you were really good at understanding the principles behind concentrations, amounts, dilutions etc., you could get a really good exam mark. On the other hand, it was possible to get a really lousy mark.

Luckily, I was pretty good at calculations, way back then and, though I*m a bit rusty due to not using this skill, can still do it when needed.

What is this all leading to? Well, I occasionally get into discussion with customers who get their calculations very very wrong, particularly when ordering oligonucleotides and planning how much they need for e.g. PCR. Usually, the problem is over-dilution. But explaining to someone that their maths was wrong when they just placed an order for 400 pre-diluted oligonucleotides, is a sensitive subject…

(If you are a fan of James Randi, you might know about his riff on the two statements never said by Ph.D.s. If not, see the video below.)

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Anyway, this posting is just to introduce you to a couple of great tools from Integrated DNA Technologies (www.idtdna.com): Dilution Calculator and Resuspension Calculator.

Article here: Easy Resuspension and Dilution of Oligos

 

 

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