(Bacterial) Small RNA Database

More Idrissa Diallo's questions See All

Positive control of the stringent response?

I wish to compare the level of ppGpp in a Wt strain and mutant. I performed my protocol with following references: Lutz Wehmeir et al, 2001; Gonzales and Collier, 2014. My question: How to make a...

01 February 2016 9,704 2 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

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

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

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

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

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

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

Robin Mjelle

I am also interested. Did you find something?

Idrissa Diallo

Hi Robin.

I have not yet get an answer about the question.. but someone suggests me :

1) RFAM database (EMBL EBI) (my final choice)

http://rfam.xfam.org/

2) sRNATarbase (for sRNA targets)

http://ccb1.bmi.ac.cn/srnatarbase/index.php

3) SRD (a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondria small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses)

https://academic.oup.com/nar/article/26/1/160/2376813/Small-RNA-Database

keep me update if you find something.

Thank you.

An Ngoc NGUYEN

Hello,

You can also check this site for a few more

https://omictools.com/bacterial-srna-data-category

Cheers

Thank you very much dear AN...

You're welcome.

Olatz Ruiz‐Larrabeiti

Hello! I am trying to access the updated version of srnatarbase 3.0 without success, does anybody know if this database is running?

Thanks in advance!

Laura Wicke

So for me it is also not working Olatz Ruiz-Larrabeiti.... Did you find a solution?