Any reliable computational tools for genome-wide screening for bacterial small RNAs?

24 June 2022 0 9K Report

I am interested in knowing the genomic presence of small RNA genes before I perform transcriptome profiling. Most of the tools I see (sRNAscanner, QRNA, sRNAPredict, are not recent or very robust. PresRAT seems great but the server is down at least most of the time (http://www.hpppi.iicb.res.in/presrat/webserver_index.html). Any recommendations would help.

Badges
Science topic

More Justin Nyasinga's questions See All

Would using an asRNA for repressing transcription of a high expression Listeria monocytogenes non-coding RNA harbored in a plasmid be a viable option?

Hello all, I am interested in deleting a highly expressed non-coding RNA located on a Listeria monocytogenes plasmid. Currently, there are not any optimized gene deletion methods for Listeria...

09 February 2021 4,994 1 View

SDS-Gel stacking gel polymerization issues?

Can anyone provide any insight as to why my Tris/Gly SDS-Gels are polymerizing slowly? This especially applies to my stacking gel (image attached) both 4% and 6%. The stacking gel wells polymerize...

24 January 2021 3,791 4 View

Will rat colon cancer cells (DHD/K12) derived from BDIX rats grow in Sprague Dawley ?

we plan to induce colon cancer by injection. Cell lines derive from BDIX rats, but our experimental setting would favour SD rats. any experience?

23 January 2021 1,437 2 View

I am interested in sequencing small RNAs in bacteria but enriching for small, weakly expressed transcripts seems to be a challenge. Any ideas?

Assays for bacterial small RNA sequencing

06 January 2021 4,549 2 View

What is the white layer on my fermented natto bean paste?

Dear all, Good day! Recently i tried to ferment my blended soya bean powder mixed with Natto bacteria culture in a Natto maker (containing some water) at around 45 degree celsius overnight....

23 November 2020 7,105 20 View

How do I extract mice brains for multiple experiments?

I am looking to complete western blot experiments and IHC experiments on the same cohort of mice. Is it possible to Harvest the mouse and use the right hemisphere for IHC and the left for western...

08 September 2020 5,436 3 View

Why the need to have CIE formula when color difference can be measured with RGB values?

Dear all, Recently i have been trying to measure colour difference between my samples. I am a little confused as to why i cannot just use the basic colours - i.e., red, green and blue to measure...

02 August 2020 7,375 2 View

Does anyone know of an Antibody against against Mouse Microglia trf2 that is good for Immunofluorescence and Westernblot?

Hi, I am studying the knockdown of Trf2 protein in Murine microglia cells invitro and wish to demonstrate this knockdown via immunofluorescence and Western blot. A dependable Trf2 antibody and...

02 June 2020 8,682 3 View

Should I use log transformed data for correction then revert it back?

Hi, I'm trying to merge two chlorophyll datasets from different sensors by applying linear regression on their data overlap. The journal that I'm following log transformed (base 10) the data from...

02 April 2020 871 7 View

How do I view a sequence aligned to a genome in IGV?

Hello, I am new to sequencing and this line of work. For the past several weeks I have been using Geneious, and have collected several sequences that I believe to be a certain protein group. I...

29 March 2020 1,189 3 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

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 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

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 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

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