Sudip Das

12 Questions 32 Answers 0 Followers

Questions related from Sudip Das

What is an accepted equivalent of non-parametric version two-way ANOVA in R package?

I use R for my statistical analysis. I want to analyse a kinetics experiment that involves measurement over 3 time points with control, genetic background 1, 2 and 3. Can anyone suggest a test and...

19 October 2016 7,565 3 View

Any experience on ChIP-Seq for Staphylococcus aureus protein-DNA binding studies ?

Hello everyone, We have been trying to find the binding site for a S. aureus regulator. The first few tries with the ChIP-seq failed. Although, normal protein immunoprecipitation with FLAG-tagged...

25 May 2016 691 4 View

Can anyone suggest cell lines to study cytokines production upon infection in vitro ?

I want to study cytokine production upon S. aureus infection in vitro. I have the following concerns: 1. Which human/mouse cells are best suited ? 2. Which assay is best suited in terms of both...

21 September 2015 4,046 4 View

What is the best strategy to catch a regulatory non-coding RNA in action ?

I am a studying a long ncRNA in S. aureus. This ncRNA is important for virulence but no molecular mechanism or interaction studies have been performed yet. This could have possible...

04 March 2015 6,417 7 View

What are major inflammatory cytokines that can be quantified upon lung infection ?

I am testing a bacterial mutant in pneumonia model and also wanted to check for inflammation. Apart from microscopic examination using HE staining, I wanted to quantify inflammatory cytokines in...

18 March 2014 1,829 5 View

Is a poly-glycine or poly-glycine/serine linker necessary with 3X FLAG tag?

I am planning to add 3X FLAG tag to a protein sequence and upon my literature search I found that there have been studies where 6 Glycine linkers were used between the protein and the FLAG tag. Is...

28 February 2014 5,764 0 View

How to get rid of DNA from agar plates?

I want to use mouse tissue homogenates containing bacteria and plate it on agar plates. For my experimental purpose I need to pool the bacteria from the plates. If I scrape off the bacteria, will...

04 June 2013 9,556 2 View

DNA eluted with 6M Guanidine hydrochloride from Streptavidin Magnetic beads, does it need further purification for downstream applications?

1. Will be compatible with Agarose TAE gels, when loaded directly? 2. Will it be compatible in Phusion PCR reactions, further as template? Note: The manufacturer recommends 6m GuHCL for elution...

16 May 2013 6,050 6 View

Which is the best method for elution of DNA (biotin tagged) from Streptavidin Magnetic Beads?

I have primers with Biotin tag. I use them in PCR for enrichment of particular amplicons. I have a feeling that the 6M Guanidine HCL recommended is not doing the best job. I also have to use the...

10 May 2013 5,473 6 View

Why does THP-1 cells shown different populations in flow cytometry scatter plot?

Hello Scientific World, I would highly appreciate some help here. I am using THP-1 monocytes as my pet cell line to generate human macrophages. Before every differentiation process, I test my...

01 January 1970 1,342 6 View

How can the expression of Interleukin-10 and MMP12 be stimulated in macrophages ?

Hello, I am currently trying to standardise qPCR primers for IL-10 expression in human macrophages i.e. checking amplification, primer efficiencies. Before the actual stimulation by bacteria, I...

01 January 1970 4,938 3 View

What is the best way to isolated RNA from tissue or preserve tissue for RNA?

Hello everyone, Being naive to the process of RNA isolation from mouse kidney, I wanted your help in adapting an optimal protocol for the following: 1. Preserving mice tissue for RNA. For e.g....

01 January 1970 3,319 9 View