QPCR primer desing?

More Andres Fernandez Gil's questions See All

Where can I find atmospheric measurement profiles (temperature, density, etc.) between 300-800 km altitude?

I am investigating thermospheric mass density profiles between 300-800 km altitude. I would like to compare the variability with other parameters, including temperature, electron content,...

01 March 2021 5,902 3 View

How to design a boost converter for a mppt controller?

I have a doubt on how to select the inductor and capacitor value when I want to implement MPPT controller. This is because we always take a maximum output voltage and current but in this case, we...

28 February 2021 3,637 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Agarose gel purification pre MinION sequencing?

Dear all, we performed an agarose gel purification with MinElute kit (QIAGEN) to extract bands between 3500 bp and 6000 bp for further sequencing with MinION. After the purification process,...

16 February 2021 5,178 1 View

How to make Fast Green FCF from powder?

Hi everyone We need Fast Green to electroporate plasmid into mice embryos, therefore we simply need it to see some color in the liquid we are electroporating so that electroporation is more...

07 February 2021 1,671 2 View

Why green band returns more inliers than NIR band during image registration?

Hello I'm using image registration over the bands of the micasense red-edge camera. Using RedEdge band as the fixed image. After removing inliers I can notice that inliers of the NIR band are...

13 January 2021 3,980 2 View

Any Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber?

Hi everyone I'm currently working with a membrane transporter protein to which I need to simulate molecular dynamics (MD). For this, I have inserted my protein in a membrane with CHARMM-GUI and...

16 December 2020 407 1 View

Jellyfish as food?

We are investigating the acceptance of jellyfish-based food dishes in Latin America. If you are interested in the topic, please fill out the anonymous survey at the following link. Thanks in...

06 December 2020 4,266 2 View

Problem executing MrBayes. Help?

Hi, I'm trying to run MrBayes 3.2.7 with a matrix of 37 species and 20561 nucleotides. I consistently receive the following error: MrBayes > Execute...

18 November 2020 3,867 3 View

Which commercial DNAse do you recommend me?

Which is the best DNAse (or DNAse kit) you have worked with? I am looking for a good DNAse that can remove DNA from an RNA sample in one pass. Material would be used for future RT-qPCR analysis....

18 November 2020 8,769 3 View

In PRIMER, is it possible to downweight certain taxa in multivariate community datasets to reflect uncertainty around identification??

I have a dataset with about 80 different species. As usual, some species are very easy to identify with certainty whereas others are more difficult, which means that I am less certain of my...

03 March 2021 8,066 4 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

How to calculate the annealing temperature of a primer pair?

I have to amplify a gene and my primers just reached. The Tm for Forward primer is 64.2, and that of reverse primer is 65.5. Can some one suggest how to get the best annealing temperature? Thanks...

01 March 2021 360 7 View

No title

Does anyone have the experience of using Taq Man probes in the QIAGEN Rotar- Gene qPCR machine?

01 March 2021 5,311 1 View

Anybody with an idea on how do design specific primers for detecting tomato resistance genes tm-1, TM-2 and Tm2^2?

I am trying to identify these 3 genes among some tomato cultivar collections and after aligning some sequences from NCBI, I couldn't find unique sequences to target for specific primers. There...

28 February 2021 606 3 View

What is the ideal efficiency for a qPCR?

hello everyone, I need to do standard curves for my qPCR, what is the ideal efficiency range? I tried a primer (Mglu2 receptor) that gave an efficiency of 90.2%. Is it accepted?

28 February 2021 1,254 3 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

EMSA troubleshooting. Protein-DNA complex not migrating, cold probe lane with multiple bands. Can anyone help?

I'm running an EMSA to show the DNA binding activity of recombinant proteins versus the Wild type. Previous assays run by my research group using a different test system show the protein-DNA...

24 February 2021 8,325 1 View

Joshua Beytebiere

Primer3Plus is what I have used in the past. I have been happy with it. It can be found here: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

Emre Bektik

You can also use NCBI primer blast tool. I feel more comfortable of using this over others. https://www.ncbi.nlm.nih.gov/tools/primer-blast/

Arman Rahimmi

Try these links:

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

https://www.idtdna.com/pages/tools/oligoanalyzer?returnurl=%2Fcalc%2Fanalyzer

https://probes.pw.usda.gov/batchprimer3/

However, I strongly recommend using oligo7 software, which is a strong tool for designing primers. It is precise, user-friendly, and have many attractive features.