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Questions related to Small RNA
Hi, It is the first time I am working with small RNA-Protein interaction. I need to design DNA template for T7 RNA polymerase to synthesize my small RNA. I just want to make sure I need to put the...
04 April 2015 6,226 6 View
I am doing an over-expression of a small RNA of less than 200bp. Firstly, I do a PCR and an electrophoresis and the intensity of the band of my RNA is good. But when I cut that band and I purify...
04 April 2015 4,743 5 View
Can anyone tell me if at the time of making libraries of small RNAs have to make 6% polyacrylamide gel and cut the band. This I could not replace purification with magnetic beads. There is another...
03 March 2015 1,236 7 View
We normally isolate RNA from rice and Arabidopsis by using trizol. We would like to do RNA-seq and small-RNA seq. There are commercial kits like miRVana which allow to isolate total RNA including...
03 March 2015 995 5 View
I know a few different methods to specifically label RNAs with fluorophores. I was wondering if I can also do this enzymatically within a bacterial system. This means I would like to know whether...
03 March 2015 1,769 3 View
OK, let's imagine you have lists (fasta files) of clean unique 18-30 nt reads with their frequences from several libraries. How do you sort our the functionally important sRNA (particularly...
02 February 2015 4,397 8 View
I am planning to carry out a miRNA expression study on my invitro cell model. Initially I had planned to proceed forward by extracting the total RNA, small RNA library prep and then proceed to...
02 February 2015 7,331 6 View
I have to do a Biotinylated RNA pull-down assay to verify the ability of two RNA binding proteins to bind RNA of interest. I’m working on designing the oligos. I wonder it is better to add biotin...
02 February 2015 3,897 3 View
I'm in the initial stages of planning a miRNA seq experiment using human cultured cells and decided on TRIzol extraction, Truseq small RNA prep kit, using an illumina HiSeq2500. The illumina...
01 January 2015 8,327 3 View
Hello, I am about to IP my protein of interest and maybe (I hope so) some small RNA would co-IP with it. Since this is my first time in this area, would anyone be so kind to suggest the best...
01 January 2015 641 4 View
Hi, I am using a miRCURY RNA Isolation Kit to extract exosomal RNA from 0. 5 ml serum and I got very low volume. Then I reduced the elution volume ( from 100 µL to 50 µL) in order to make it more...
01 January 2015 9,915 4 View
Any help would be much appreciated.
01 January 2015 2,422 2 View
I'm going to use small RNA sequencing data from GEO available at NCBI for predicting new miRNA's, but the format of datasets at GEO are .soft and I don't know how I can extract small RNA sequences...
12 December 2014 4,499 1 View
I'd like to see if either microRNA or siRNA affects the translation of my gene of interest (protein). I understand that there are kits which detect small RNAs from total RNAs but how can I...
12 December 2014 544 7 View
How do small RNA- and DNA-Oligos (~20nt) differ in their electrophoretic mobility under denaturing conditions? I was just wondering whether there is a general difference in the migration of...
11 November 2014 8,852 4 View
Hi, So I am interested in a way for generating DNA, smallRNA and mRNA from the same biological sample for NGS (ExomeSeq, smallRNAseq and RNAseq). Essentially I am looking for a protocol/kit that...
11 November 2014 2,165 8 View
Hi guys, I'm going to perform a KD of my protein of interest. The problem is that I'm working with suspension cells. Could someone suggest a protocol avoiding electroporetion? thanks
10 October 2014 5,274 6 View
I am trying to transfect BMDM with plasmids (no small RNA) but I found few papers doing this. Any successfull protocol to follow?
10 October 2014 8,302 3 View
I'm looking to isolate the total RNAs from yeast and then prepare them for RNA-Seq. I'll be testing the quality of the RNA with a bioanalyzer. But it seems that most options degrade the RNA or are...
09 September 2014 6,015 5 View
I am going to profile microRNAs by small RNA sequencing. The starting material that is going to be used for microRNA isolation is too small. So we decided to isolate small RNAs by three different...
09 September 2014 9,306 9 View
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 10,032 3 View
Modification can ant Post translation modification (PTMs) in RNA e.g methylation etc. Subtype can be mRNA, miRNA, rRNA, lncRNA, small RNA etc.
08 August 2014 2,866 4 View
I have a 27 nt siRNA that is cleaved by DICER enzyme into a smaller 21 nt fragment. Due to physical and chemical modifications, this 27 nt will be cleaved on an exact point and will originate a...
08 August 2014 3,213 3 View
I have an RNA-seq from Illumina 100 pb PE. My aim was to search for DEG, therefore RNA extraction protocol was focused on mRNA enrichement. Now I'm curious to check for small RNAs. Is there...
07 July 2014 5,398 7 View