What is the best & easiest way to design QPCR primers for Arabidopsis genes?

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Will my DNAse treatment breakdown all the DNA if I add the EDTA before the 37C incubation?

I am currently using Ambion DNAse to remove any DNA contamination from my RNA samples. The protocol requires a 37C incubation for 30min and then a 75C incubation for 10min to deactivate the...

08 September 2013 8,465 5 View

How do you quantify a microRNA?

I've read various papers on how to quantify microRNA by stemloop PCR and other QRT-PCR machine based methods but none ever explain how to design the primers or other essential details.

07 August 2013 2,444 5 View

How does one over express a microRNA?

I've identified some microRNAs that I think are interesting. I would like to over express them with a 35S promoter but don't know where to begin? I have a destination vector with the promoter, so...

07 August 2013 9,244 5 View

I have some Arabidopsis genes that I'm interested in, is there a way to easily identify if they are in a family or have any homologues?

I've tried blasting the translated sequence that provides some information, i've looked at the TAIR website (http://www.arabidopsis.org/) and the biofuel feedstock genomics resource which produced...

02 March 2013 8,694 5 View

No title

I want to create RNA and miRNA libraries for the Arabidopsis root tip and was wondering how many plants i should grow during my experiment?

03 April 2012 3,338 10 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

Does anyone have a recommendation for yeast reporter gene plasmid/protocol?

Hi, could anyone recommend a plasmid and/or protocol for reporter gene assay in S. cerevisiae? I want to assess the effect of growth conditions on a transcription factor, so I want to clone it`s...

01 March 2021 210 1 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

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

Genescan gives 3 peaks instead of one?

Hi all, I am doing a genescan analysis for a deleted exon in the patient sample. The amplified region is 215 bp. In the patient sample because of homozygous deletion, no peak is observed while in...

23 February 2021 5,645 1 View

Khaled Said Ali

Hi dear, you can use genbank datebase for design primers by some aligment.

Mingqi Zhou

I often use IDT tool (http://www.idtdna.com/scitools/Applications/RealTimePCR/Default.aspx), which is powerful and easy to go.

Julia Swan

Hi - this is a usefuel article: https://bitesizebio.com/2504/read-this-before-you-design-those-qpcr-primers/