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

More Richard Barker's questions See All

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 8,500 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 2,487 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 9,282 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 8,732 5 View

How many Arabidopsis root tips will be needed to generate 25 µg total RNA, so that the mRNA can be used for RNAseq? Will this be the same for miRNA?

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 3,373 10 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Anyone having idea about VN primer for miRNA primer design ?

How to design VN primer to attach with universal reverse primer

05 August 2024 2,116 3 View

The Optimal Experimental Approach for Gene Function Analysis?

What is the most suitable experimental setting to understand the consequences of a particular gene: (1) targeted degradation of the specific transcription factor (TF) of the gene, followed by...

04 August 2024 6,265 1 View

I'm optimizing a tetra-ARMS PCR protocol with amplicon sizes: 165bp, 123bp and 93bp. Why, in the gel, only 165bp is visible while I'm expecting all 3?

It's an end-point PCR protocol. I'm using 1.5% agarose gel with SyBR Safe dye and TBE as a running buffer, visualization on BioRad XR+ system. I was primarily thinking of primer efficiency,...

01 August 2024 4,673 4 View

PCR showing no bands - Master mix and primers didn't mix?

Hello everyone, I performed a PCR yesterday, and the results showed no bands on the gel. Of course, I probably missed some crucial steps, like adding my samples to the PCR strips themselves, for...

31 July 2024 2,406 6 View

How to we see transcription activity of the bhlh79 family is at the N-terminal or C-terminal?

I'm a PhD Student. From Northwest Agriculture and Forestry University China. My Problem is this I start my work on bhlh79 transcription factor gene. I do my Y2H 5 time but the colonies appear on...

30 July 2024 1,412 8 View

When should I stop watering A.thaliana for collect their seeds?

I have been following Rivero et al 2014 protocols, but I am not sure when I should stop watering because my plants are completely yellow but the siliques are not 80% brown. Any recommendations?...

30 July 2024 2,301 7 View

How to retain amplicon yield after Ampure bead cleanup, following a 2-stage PCR protocol?

Hello all, I have been trying to follow a 2-stage PCR protocol used to amplify barcodes of a large yeast library, as per Nyugen et al. (2022) -...

30 July 2024 841 2 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/