Is there easy and reliable online software for estimation of RNA-protein binding efficiency?

Hello Everyone, I would like to check if my protein of interest can bind to RNA of interest. Before moving forward I would like to check using any available prediction software. Please let me...

11 December 2019 6,137 3 View

How much RNA typically we can get from single cell?

How much RNA typically we can get RNA from any single cell? Has anyone isolated RNA from single cells? Using which method or protocol? Based on your experience, what possible downstream assays can...

06 July 2018 5,118 8 View

What are exosome negative markers?

Hi, I am relatively new to the exosome/MV study. I would like to know which proteins and RNAs are absent (or likely to be absent) in exosomes/MV (negative control). I am aware about the...

11 December 2017 3,116 5 View

Is it possible to see eukaryotic cells with attached fluorescent-bacteria in FACS analysis?

11 December 2016 6,773 5 View

Is "Cumulative Thesis" recognized everywhere?

02 March 2016 2,563 0 View

What is the best method to obtain single cell suspension of BCG?

I am looking for protocol or methodology to obtain single cell suspension of M. bovis BCG. Normally they occur in clumps when I see them under microscope. I found some methods like Sonication,...

11 December 2015 9,391 3 View

Is there any database or online search tools available to find genes/chromosomes which are targeted by known long non coding RNA?

Finding Long noncoding RNA targets.

07 August 2014 5,036 5 View

In target prediction, what is the basis for miRmap score selection?

As you can see in screenshot final miRmap score is 80.06, but in the explanation section it gives two target sites with two different miRmap scores (55.50 and 75.51). How is the final score...

04 May 2014 2,355 0 View

How to intersect more than 10 non numerical data sets?

I have more than 10 sets of non numerical data and want to find out common element present in all sets. How can I achieve this, or which software is helpful?

10 November 2013 5,302 7 View

What is the shortest nucleotide sequence we can map with confidence?

I have a NGS RNA seq data and would like to search RNAs and their expression profile. I would like to know what is the shortest RNA (shorter than miRNAs) that can be identified as a RNA species....

01 January 1970 8,992 4 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 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

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

How do I transfect a large plasmid into PC12 cells with nerve growth factor (NGF) receptor?

I have a large 16 kb plasmid, which I need to transfect into PC12 cells. Lipofectamin 2000 didn't work and with GFP alone the transfection rate is very low. I also tried the neon invitrogen...

25 February 2021 6,635 5 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View