What are tools available for identifying differentially expressed miRNA from the read count data?

More Rucha Wadapurkar's questions See All

How to visualize binding site residues of docked complex in Pymol?

I have created docked complex.pdbqt file using Autodock and I have uploaded that file in Pymol and visualized formed hydrogen bonds between ligand and protein, but the binding site residues of...

02 March 2019 4,151 4 View

In clinvar database,using variation viewer,how to visualize only those mutations in .vcf file,as all mutations are displayed in bottom table?

After uploading .vcf file of identified mutations using Variation viewer tool in ClinVar database, all mutations are displaying in bottom resultant table, apart from those which are present in...

11 December 2018 9,563 0 View

Molecular dynamics errror of Gromacs 5.1.1 using Force Filed Amber?

gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (solv_ions.gro, 63371)does not match topology (topol.top, 63831). other...

04 May 2018 9,814 2 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

Can MicroRNA cross the blood brain barrier?

In diseased conditions, many genes and gene products are visible in the bloodstream. So my question is whether we can find traces of microRNA which is involved in disease and disorder in blood serum?

24 February 2021 7,064 3 View

Are exogenous molecules transferred between human cells during doubling ?

Hello RG community, I wonderer whether exogenous molecules (e.g. reporter plasmids, miRNAs or other artificial molecules) are transferred between cultured human cells during their doubling ? So,...

21 February 2021 6,633 3 View

Has anyone encountered any problems with abm good microRNA primers for quantification of mature miRNAs?

I've been trying to quantitate mature microRNAs in 293T cells with and without 'X'. 2ug of total RNA (isolated by Trizol method) is converted to cDNA using All-in one microRNA cDNA synthesis kit...

17 February 2021 8,986 2 View

What is the best way to fix plasma derived miRNA for subsequent cDNA synthesis?

I need to quantify blood plasma derived miRNA through q-RT-PCR. For this I need to fix RNA content in my cDNA reaction. What is the best way to do this? Currently, I take readings of my plasma...

03 February 2021 9,330 3 View

What is the general miRNA yield one gets from the Qiagen miRNEASY serum/plasma advanced kit?

I am using the Qiagen miRNEASY serum/plasma advanced kit, using 400ul of frozen plasma. What is the yield you get on average? I am using nanodrop currently for quantification. I am getting...

02 February 2021 8,806 2 View

Which miRNA arm is a right target for analysis, 3p or 5p?

I'm working on selecting mouse miRNAs to analyze and stumbling upon one confusing issue, some of the papers do not specify which arm they analyzed and they just state something like " miR-34a was...

16 January 2021 3,792 4 View

Is negative controls necessary for western blotting?

I am trying to confirm my miRNA target by western blotting. I have a ds mimic and a ss inhibitor of my miRNA. Is it necessary to use negative controls for mimic and inhibitor? If yes, how can I...

09 January 2021 2,320 3 View

Can I predict miRNA by knowing the mRNA target?

Hello! I am trying to predict in silico the miRNA by knowing the target. Most of published research starts by knowing the miRNA and predicts the target using online tools. Are you familiar with...

31 December 2020 7,433 5 View

What are the possible drawbacks of using miRNA sponge to enhance the specificity of gene expression?

I am searching for miRNA repeats put between WPRE and 3'LTR of my lentivirus, in order to enhance the specificity of transgene expression in human neuron cells. But if clinically translation of...

26 December 2020 9,921 2 View

Iman Hassan Ibrahim

I'd come across a paper using R package edgeR for the same purpose.

As an alternative, you may try this

http://bioinfo.cipf.es/noiseq/doku.php?id=start

Do Ngoc duy

Hi,

There are many such as https://www.mirnet.ca/

Also you can use some package in R such as EdgeR or Deseq2 to perform DE analyses.

Laurent Guyon

Analyzing through R (through RStudio) would definitely the best idea - it requires just a bit of work to get in, but worth to do.

After having the Differential Analysis values (DE = log2(expression/ctrl)), I would suggest miRViz, which we recently built, to interpret the dataset:

http://mirviz.prabi.fr/

quick video tutorial: https://www.youtube.com/watch?v=vrwB1hbcjyQ

bioRxiv: https://www.biorxiv.org/content/10.1101/813550v1

MiRNet is great too, and complementary to miRViz: https://www.mirnet.ca/miRNet/home.xhtml

Both would be useful for you. No need for computational skills. I would suggest first miRViz, and then miRNet.

'hope this will help you.