How to design best primers to amplify a region in mice genomic DNA?

More Lakshani Perera's questions See All

How to clone the GOI into ROSA26 donor plasmid?

I am new to CRISPR Knock In. I want to clone a gene into ROSA 26 donor plasmid to Knock In a gene into the mouse genome. I have selected the addgene plasmid # 74285. But I cannot figure out where...

09 October 2019 9,506 1 View

Hello, I have a CRISPR related question. Can anyone help me?

I wanted to knock out MSH2 in mice cell line CH12F3 and after gRNA construction, transfection and single cell sorting, I got single colonies. I used two guide RNAs to give a deletion but when I...

04 May 2019 8,042 6 View

No title

for recombinant proteins do we have to use specific antibodies?

03 April 2019 9,757 3 View

How do I amplify a 7.4 KB fragment in mouse genomic DNA ?

I am struggling to amplify an 7.4 kB fragment which I need to confirm my CRISPR KO. I have tried Pfu and Phusion polymerase, used both HF and GC buffers, tried 50 - 70 C temp gradient, DMSO...

02 March 2019 1,361 4 View

Anyone familiar with DBCO -CY5?

I need to purify DBCO CY5 since it give lots of unwanted bands when run on PAGE. I am looking for a protocol for that.

01 January 1970 239 5 View

Can anyone suggest me a method to analyse altered replication dynamics other than DNA fiber analysis?

One of the compounds that we synthesized in our lab can result in replication fork collapse. We have tested for gmma H2AX foci that shows the ds strand breaks. But we need to test for the...

01 January 1970 6,392 0 View

Has anyone tried using zeta probe membrane in DNA slot blotting?

I do slot blotting to my DNA samples that contain Carboxy rhodamine tags and then scan through typhoon (CY2) to get the signal intensity. Unfortunately membrane looks terrible and I cannot...

01 January 1970 2,833 0 View

Can anyone suggest me a suitable solvent system for Cl and azide separation where both are linked to n-hydroxyphthalimide with an ethyl group?

Cl and azide linked to n-hydroxyphthalimide

01 January 1970 1,790 2 View

Can anyone help me with this Urea-PAGE gel issue?

When I run my 17mer DNA oligos on PAGE gel I can see a smear above my DNA band. Does anyone know a possible reason or how to minimize this? I have attached a gel image here as well. Thank you

01 January 1970 876 4 View

Can anyone help me with this question?

what is the most reasonable mechanism for hydrothiolation of terminal alkynes?

01 January 1970 7,687 0 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 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 know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 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

Abhijeet Singh

Genomes for selected organisms (primary reference assembly only)

Frederic Lepretre

Hi Lakshani,

Md Abdur Rahim send you a good way to test your primers once you'll get the sequence from the same website (http://genome-euro.ucsc.edu). choose your species and target and you'll arrive at the right place to download the genomic sequence.

fred