Swati Megha

14 Questions 19 Answers 0 Followers

Questions related from Swati Megha

What length of long non coding RNA (lncRNA) should be used for its overexpression in plants?

Hi all, I am planning to over-express a lncRNA (under 35S) in Arabidopsis. Will the presence of 20-30 bp sequences upstream and downstream of lncRNA sequence affect its over-expression? I...

08 August 2019 6,955 1 View

Is there any online tool to make delta SNP index plots?

HI Research family, I am trying to construct delta SNP index Manhattan plots. Are there any stand-alone or online software for it! I am looking for something that doesn't involved programming....

05 May 2019 2,966 4 View

What should be the path length when doing enzyme assays in 96 well-microtiter plates?

Hello Everyone, Can someone please tell me path length to be used in the calculations when 96 well plate is used for assaying the activity of enzymes! I assume we dont use 1cm path length as in...

07 July 2017 9,812 9 View

Over-expression of pre-miRNA not translated into increased expression of mature miRNA?

Hi everyone, I have cloned precursor sequence of a miRNA (say mIR1) in Arabidopsis and generated three independent, homozygous transgenic lines in Arabidopsis. When I performed qRT-PCR of these...

04 April 2017 5,231 15 View

What is the difference between over-expression of miRNA and Artificial miRNA technology?

So, over-expressing a particular miRNA most probably will cause down regulation of target genes. Also, with use of artificial miRNA, we are overexpressing the miRNA and thus causing silencing of...

03 March 2015 6,299 11 View

How can I normalize the sequencing data in two different libraries?

Hi Everyone If I have data from four miRNA libraries. One of the libraries have 4 times more reads than other three libraries. How will the data be normalized among different libraries? People use...

03 March 2015 1,972 8 View

How can I find the 1kb upstream region of miRNA precursor gene in Brassica napus?

Hi Everyone, I am trying to find stress responsive cis elements in the upstream regions of miRNAs in Brassica napus. miRbase gives me the genomic coordinates of miRNA precursor gene, but I am not...

12 December 2014 5,489 2 View

Can housekeeping genes (actin, GADH,UBC9 etc.) be used as an endogenous control for plant miRNA qPCR?

Hi Everyone I have tried using U6 and 5.8sRNA as endogenous control. Although the expression of both these remain constant in different conditions, the Ct values for U6 are quite high (30 or so)...

11 November 2014 10,055 5 View

What does the +/- sense of orientation actually mean and what is its implication in determining miRNA precursors in plants?

I have a number of miRNA precursors. These are the ones that mapped to a concatenated genome consisting of B. napus EST, B. oleracea EST and B.rapa genome. Some of the precursors have mapped to...

11 November 2014 5,174 1 View

How should I interpret plant miRNA data? When doing clustering of miRNAs in families which sequence should I use?

Hi everyone I am doing a next gen sequencing project to identify miRNA in brassica. I made the small RNA libraries and sent them for sequencing and subsequent analysis. The data that I got back...

09 September 2014 9,888 3 View

How important are A260/A230 and 28S/18s ratios for RNA that are to be used for miRNA deep sequencing?

I did an RNA isolation by TRIzol method from canola plants. When measured by NanoDrop 1000 the A260/A280 ratios for RNA were between 1.7-2.0 while the A260/A230 ratios were between 0.7-1.5. Though...

08 August 2013 6,848 35 View

Can someone advise on whether I should use miRNA Deep Sequencing- Pooling or not?

I am designing a experiment to identify miRNA in Brassica. From what I have read in the literature, most of the authors do not mention about pooling the samples/RNA from biological replicates. I...

07 July 2013 4,071 4 View

Can Real time kinetic analysis kits available in the market serve the purpose of determining the ribonuclease activity of a plant protein?

I am planning to determine the RNase activity of a protein (provided it has this activity!). Will it be sufficient to determine RNase activity through Real time kinetic analysis kits available in...

12 December 2012 7,509 1 View

How well can the gene expression measured by qRT be correlated with the protein levels?

A gap between the mRNA and protein levels exists because of various levels of regulation. So, exactly how well can the gene expression measured by qRT be correlated with the protein levels?

12 December 2012 587 37 View