16S RNA Database - FAQS.TIPS

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What are all the recent trends in sample collection and DNA extraction for genome analysis?

Methods of DNA extraction from human samples especially blood has different methods such as: 1)Solution based extraction using organic solvents. 2)Solution based extraction using salting...

05 June 2018 3,219 0 View

UGC CARE list journals

How many journals are listed in UGC-CARE and name of journals in CARE list indexed in SCI and SCOPUS?

01 January 1970 3,864 2 View

What are the possibilities of changing a fish's color for longperiod of time?

The fishes color is changed naturally due to adaptation and reproduction through chromatophores but changing the color of fishes for ornamental purposes are increasing therefore synthetic coloring...

01 January 1970 6,015 6 View

Journal publication cost and duration

How long does it take to publish in UGC-CARE listed journals and their price range.

01 January 1970 7,456 1 View

How long does the protein sample remains stable at deep freezing after extraction?

The extracted protein from a plant sample was immediately dried and stored in deep freezing condition at -80°C. How long does this remain stable until estimation and analysis?

01 January 1970 4,755 1 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

06 August 2024 807 3 View

RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

I am planning to collect human fecal samples for metatranscriptomic analysis using MGI. These samples are from indigenous people living in a region with high temperatures. I will have access to a...

06 August 2024 1,367 3 View

Do you have good tips for seaweed tissue preservation in the field for post RNA extraction?

I will be with my students collecting seaweed samples in a marine farm and later we will process this tissue for RNA isolation and further sequencing. Does anyone have tips on how to collect the...

04 August 2024 501 2 View

What is the acceptable p-value cutoff for GO enrichment analysis ?

I have an RNA-seq data that I have analysed using Limma-voom and have extracted the gene IDs, log2FC and the p-values. At p value < 0.05, I have over 10,000 DEGs, however, when I run the GO...

31 July 2024 225 2 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

How to prediction 2D to 3D aptamer?

Hello, I have a little problem. Well, right now I only have the DNA aptamer sequence. I went to see the 2D model form with DNA folding. After that, I used RNA Composer to simulate in 3D and used...

30 July 2024 6,794 0 View

Balig Panossian

You could use the NCBI 16S database for microbes as it is well curated.

link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz

The best tool to annotate the genome of a parasite would be Companion by Sanger

link: Article Companion: a web server for annotation and analysis of paras...

Abhijeet Singh

I would recommend arb-silva for the 16s sequences. It has several functionalities and software for the NGS data analysis and classification. You can also try RDP database. Both these are curated databases and offers many possibilities for the users.

Aishwarya Amirdharaj

Thank you all...