How to shortlist sequences for phylogenetic tree?

I want to construct a phylogenetic tree using almost 2000 sequences from prokaryotes as well as eukaryotes. To simply the tree, I would like to shortlist the sequences. What is the best way...

06 July 2017 3,856 5 View

How can we check chemical modifications in DNA or RNA?

What are the methods to check chemical modifications in DNA or RNA? By chemical modifications I mean formation of some other compounds on reaction with other metabolites, or some external...

04 May 2016 4,839 4 View

Positive controls for qPCR for Ca2+ and MAPK signaling in plants?

09 October 2015 1,433 1 View

Why is phosphate buffer prepared by mixing K2HPO4 and KH2PO4?

We mix the two solutions in appropriate ratios to get the desired pH buffer. Why can't we adjust the pH using NaOH or HCl?

08 September 2015 7,850 1 View

What's the best way to crush plant leaves for genomic DNA isolation using Qiagen DNeasy kit?

03 April 2015 5,858 14 View

Can someone please distinguish between ML, NJ, ME and MP?

MEGA software gives different options for tree construction. Can someone please explain when to use which tree? I read literature but couldn't understand clearly. Please suggest some literature...

03 April 2015 9,870 0 View

How do I PCR amplify AT-rich sequence from genomic DNA?

02 March 2015 6,445 7 View

Does anyone have a recommendation for yeast reporter gene plasmid/protocol?

Hi, could anyone recommend a plasmid and/or protocol for reporter gene assay in S. cerevisiae? I want to assess the effect of growth conditions on a transcription factor, so I want to clone it`s...

01 March 2021 210 1 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 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

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 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

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 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

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View