Small RNA

What is the optimum read length required for a illumina based small RNA sequencing?

I am planning to pursue a small RNA sequencing project, however, I am a bit under confident in choosing the correct read length for a illumina hiseq based small RNA sequencing. The options that I...

07 July 2014 4,160 6 View

Is anyone familiar with 30 nucleotide peak in small RNA libraries?

I performed an RNA-seq experiment and observed an unusual size distribution of small RNAs (image attached). I was wondering if anyone has seen this before. I used Ambion's mirVana small RNA kit...

05 May 2014 6,951 3 View

Which pipeline or approaches to predict sRNA's in bacteria?

I'm trying to predict some sRNA's (small rna's) which are non-coding rna's in bacteria. I'm following an approach that i have seen in a paper, that uses MAUVE and RNAz to predict them. But the...

08 April 2014 5,986 2 View

Which pipeline or approaches to predict sRNA's in bacteria?

I'm trying to predict some sRNA's (small rna's) which are non-coding rna's in bacteria. I'm following an approach that i have seen in a paper, that uses MAUVE and RNAz to predict them. But the...

04 April 2014 5,691 2 View

Which tools are there to find non-coding RNAs in bacterial RNA-seq data?

I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find some tools but I'm still quite lost (see link below). I've also seen this Biostar...

03 March 2014 4,383 2 View

What is the best protocol for purifying small RNAs for small RNA-seq in C. elegans?

I have tried to enrich for small RNAs from total RNAs using miRvana kit from Ambion. It definitely got rid of a lot of types of RNAs including abundant rRNAs, but I got enrichment of 90nt size...

03 March 2014 1,211 3 View

How to assemble 18–26nt sRNA from virus into larger contig by the Velvet software?

who can help me analyse sRNA data?

09 September 2013 6,210 1 View

How can one modify an RNA oligo to have a 5' triphosphate?

For my project, I need to cap synthetically prepared RNA oligos and most of the capping kits available require a triphosphate group at the 5' end as a substrate. I have looked all over for kits...

09 September 2013 5,715 1 View

Has anyone ever used the miRcode for target prediction?

Has anyone used this http://www.mircode.org/mircode/index.php for target prediction? If so, any comment on how it performs? eg. compared to the usual TargetScan.

05 May 2013 5,899 0 View

Which concentration of denaturing PAGE can differentiate 21nt sRNA and 24nt sRNA?

sRNA

04 April 2013 4,039 1 View

Do I really need to DNase treat my small RNA sample before library prep?

I have isolated RNA shorter than 200 nts. On an agarose gel I cannot see any genomic DNA, but this is not very sensitive. I do not want to treat with DNase because I am afraid of three things: 1)...

01 January 2013 5,920 5 View

Does anyone know how I can get small RNA seq from GEO Database? Thanks

I'm trying to find a small RNA sequence dataset that is available for download that was made from an Ago2 mutant animal or cell line.

01 January 1970 3,071 2 View

-ve RT is important in case of small RNA amplification using total RNA. How to get rid of similar amplification in this case

Small RNA

01 January 1970 4,023 0 View

Working with PCR plates for large-scale preparation of cDNA libraries for sequencing?

Hi, Does anyone have experience with preparing cDNA libraries from small RNA, for next-generation sequencing? If so, has anyone tried doing it in PCR plates instead of strip tubes? I have a large...

01 January 1970 9,739 3 View

Please suggest troubleshoot for northern blot by fluorescent probe (cye5). How did i get small RNA band complementary to my probe in Nylon membrane ??

I am trying to do northern blotting of small RNA (E.coli) using RNA blot(Bio red).Total RNA had loaded in 6% urea gel and transferred to a membrane (Amershon- H+ Nylon membrane-GE health care)....

01 January 1970 4,199 0 View

Statistical significance of find a certain number of reads in a certain number of bases

I´m working with small RNAs which are produced by transposons, in my data set I have different transposons with different sizes, by chance I expect that transposons with more bases could produce...

01 January 1970 8,763 2 View

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01 January 1970 3,118 0 View

Does anyone know how I can get small RNA seq from GEO Database? Thanks

I'm trying to find a small RNA sequence dataset that is available for download that was made from an Ago2 mutant animal or cell line.

01 January 1970 4,620 2 View

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01 January 1970 8,181 0 View

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01 January 1970 7,097 0 View

Weird 8bp peak in (clean) small RNA data? | ResearchGate

Hi everyone, I've received some small RNA sequencing data from a collaborator and after removing adapter and trimming (with TrimGalore) i have a small peaks at ~20 and 30 bp, as I was expecting,...

01 January 1970 9,693 0 View