SiRNA design tools?

More Prabhash Jha's questions See All

What could be reason for getting such type of graph for complex impedance in case of polymer blend films?

Its effect appears in real part of ac conductivity also. Can anyone suggest any reason behind it?

26 February 2021 3,487 3 View

Does behavior (shy vs bold; rare vs abundant) and flock size (small vs large) of bird species play role in niche partitioning among sympatric species?

Sympatric birds may avoid competition via multiple strategies - by different activity period, different diet, different microhabitat etc. Has any one looked into behavior of sympatric birds as...

11 January 2021 9,600 1 View

Which type of polymer is used in base boards of Printed Circuit Boards (PCBs)?

I want to know about the type of polymers in PCBs.

25 May 2020 9,640 15 View

Dear Peers! Could you please oblige me with your knowledge on vulture?

I am looking for proverbs and idioms or any short story mentioning vulture in any language or locality with English translation.

24 February 2020 2,004 9 View

I am supposed to develop a psychometric employability assessment. Any literature or advice that could help me? Also, how do I ensure honest answers?

I have never done this before. So far I have collected scales for different factors after detailed research. I plan on taking items from them and maybe restructuring them to make a proper...

31 January 2020 9,923 2 View

Which funding agency in India will grant traveling allowance for international conference in finance ??

I get an opportunity to present my paper in international conference on June 2020. I am research scholar in management (finance department).Kindly let me know which funding agency will grant...

07 January 2020 7,040 1 View

Can anyone suggest me a solver for binary linear multiplicative programming problem?

The example case is as follows: Maximize(a1 * X1 + a2 * X2 + a3 * X3 + a1 * a2 * Y12 + a1 * a3 * Y13 + a2 * a3 * Y23) constraints are: a1, a2, a3 are binary variable belongs to [0, 1], and a1 + a2...

23 December 2019 5,912 4 View

How can we estimate Nitrogen (N) in sugarcane field using satellite imagery?

I want to estimate nitrogen (N) content in the sugarcane fields using sentinel-2 optical data (Multi spectral Imagery). I have read few papers where simulated values helped in potatoes and other...

16 May 2019 4,580 6 View

How can we download the all the clean drug like compounds from Zinc12 database?

http://zinc.docking.org/subsets/drug-like When I click on sdf/mol2 format , it gives me usual.sdf.bat or usual.mol2.bat. How I will use these file to retreive the compounds????

08 April 2019 2,042 1 View

Bacterial Growth Concern ?

hi All , i am using Rhizobium species for Atrazine (as nitrogen source )removal in MS medium, unfortunately from last week its not showing growth in liquid medium while some bacterial colonies are...

25 February 2019 420 3 View

Does RNAiMAX transfection reagent work in serum free medium?

I diluted siRNA and RNAiMAX in opti-MEM and added to the cells which they were in the growth medium. Is it a right way? or should I culture cells in the opti-MEM medium for a while and not in...

26 February 2021 10,041 3 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...

22 February 2021 9,873 3 View

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 View

SiRNA transfection efficency and results interpretation ?

i am having a problem with the transfection of 2 siRNA , one for the longer isoform U and the other one of the sliced isoform S that is also the only transcribed. i am trasfection siRNA with a...

11 February 2021 8,145 3 View

Why do I see variability in mRNA expression in qPCR of the same gene (ubiquitin)?

Hi everyone! I use HaCaT cells and i transfect them with siRNA. After 48 h I extract proteins with Laemmli and RNA with trizol. I proceed with western blot to check proteins levels (and they are...

26 January 2021 5,738 3 View

Measuring small RNA abundance, without sequencing?

Dear all, Do you know any reliable and fast method to measure the levels of plant small RNAs (21,22 and 24 mer)? I am interested in only comparing the abundance of those small RNA between mock...

21 January 2021 4,002 6 View

Which is best tool for alignment of large bacterial sequence?

Hi! I need to align big fasta files (bacterial 16S) . I have tried to align them in some web-servers and freeware, but my files are too big to be run in there. I will be very glad if you could...

16 January 2021 1,266 4 View

What will be the life of siRNA (liquid form) at -20 degree, if kept unopened?

Hi all, I just want to know that, if we keep the siRNA in a -20 degree freezer (as mentioned in the product detail), what will be the average life of the siRNA? Can we store for more than one...

10 January 2021 6,346 6 View

Difficult to silence gene?

I have been trying to silence a gene of interest but I could not get silencing efficiencies beyond 50% My method of detection is via RT-qPCR and samples were extracted 48hrs post transfection. Are...

09 January 2021 3,404 4 View

Can I use FACS to optimize transfection by using a fluorescently labelled siRNA?

Dear all, I wish to find the optimal siRNA tranfection properties for my cell line. I have a fluorescently labelled siRNA which I plan to transfect by using different agents and quantify by using...

28 December 2020 5,349 7 View

Chandra Pal Singh

Dear Prabhash,

Following are the most used tools, you can use couple of them and compare output.

https://eu.idtdna.com/site/order/designtool/index/DSIRNA_CUSTOM

https://rnaidesigner.thermofisher.com/rnaiexpress/

http://dharmacon.gelifesciences.com/design-center/

http://www.protocol-online.org/prot/Research_Tools/Online_Tools/SiRNA_Design/index.html

Thanks

CP Singh

Prabhash Jha

Thank you Chandra. I will surely use the suggested softwares.

Sasa Stefanic

Try Primer3 online tool:

http://bioinfo.ut.ee/primer3-0.4.0/

We used it with success in or study on RNAi in S. mansoni on multitude of gene transcripts.

Best wishes,

Sasa

Thank you for sharing the information Sasa.