Question

Question for the smart people about short interfereing RNAs:

Is there any way to apply high through-put sequencing or transcriptome analysis to siRNAs?

Thank you in advance for your assistance!

Answer 1

may i help

Answer 2

@Kainui

Answer 3

@mrdoldum @Frostbite

Answer 4

There are methods of high throughput RNA sequencing. There plenty of methods for using genomes and transcriptomes to ID siRNA pathways. Just go to google and start looking. If you are up to research paper reading go to scholar.google.com and search around.

Answer 5

Thank you, mrdoldum. I'm really good at RNA Seq analysis, particularly the bowtie, tophat, cufflinks pathway. But I left the field a few years ago and find myself back in it suddenly. I have done some reading on PubMed and am aware of some of the options; however, I put it out there in case any of the grad students on this site have any specific particular ideas in mind.

Answer 6

@thomaster

Answer 7

What exactly are you wanting to accomplish?

Answer 8

@mrdoldrum, I am retired molecular biologist and one of my friends was diagnosed with cancer.

In absolutely the worst style of research science and the best interest of trying to save my friend's life, my friends and I have pooled our money to get the tumours and my friend's genomes (specifically exomes, not whole genomes) sequenced. And to get some form of expression level data on the transcripts - either full blown RNA Seq despite its almost prohibitive cost, or use a 3' fragment library which would not give us variant analysis but would be good (better actually than standard RNA Seq) to look at differential expression.

So, I have spent much time on the literature and on the pathway databases. I have looked at sequence level data from cases with the same cancer. It's probable that this cancer is driven by Myc over activity (not mutation, the mutations are in Myc's regulators) and that inhibition of CDK1 in particular will completely inhibit Myc and cure the cancer.

CDK1 is regulated by many proteins but also by a large, incompletely characterised and poorly understood cloud of non-coding RNA actors. Hence my question - is there any way, computational or experimental, to use transcript level RNA data and exome level sequence data to analyse ncRNA levels?

Given that we do not have $15,000 for the experimental assays we'd love to use, and given that we have 6 weeks to collect samples, sequence the samples, analyse the data, pick chemo drugs, dose them in a weak patient and hopefully save his life not kill him.

"Go do your own google searches" is a good answer for lazy kids trying to get someone else to do their homework, it's not of interest to me. Real ideas would be appreciated.

Answer 9

@shrutipande9

Answer 10

let me see what i can find for u...i am not an expert in this....mrdoldum can tell u way better...but if i come up wid something i will write to u