Swarnali Kar

19 Questions 36 Answers 0 Followers

Questions related from Swarnali Kar

How to save Bar Chart and Pie Chart from PANTHER - GENE LIST ANALYSIS?

I am trying to analyze RNA seq data using PANTHER DATABASE. When I submit a list of differentially altered genes for 'Functional classification viewed in graphic charts', it generates graphs but I...

15 April 2021 7,189 4 View

Why TSP peak height seem to vary from spectrum to spectrum in 1D 1H NMR metabolomics?

I acquire 1D 1H NMR spectra of metabolite extract using 100% D2O in 700MHz Bruker Avance set up . Now I am facing an interesting problem.-TSP peak height/ intensity seems to be different in every...

25 November 2019 1,598 8 View

Is Co-immunoprecipitation (Co-IP) enough to observe whether two DNA binding proteins bind DNA independently or they interact with each other?

I am working with two DNA binding proteins and they bind at the promoter region of a protein. I want to see whether one protein recruits another or they independently interact with the DNA.Is...

19 December 2018 9,649 6 View

Bands in western blot are behaving like GHOST!!!!!!!!!!!!!!!!!?

I am doing western blot and after development I can see that one/ two lanes have no band. Perhaps, next day I am doing same gel run with same sample with no change in protocol, this time another...

26 September 2018 8,521 3 View

How to do manual peak fitting and quantification in chenomx software?

In metaolomics 1. Regarding manual peak fitting of metabolites - We use chenomx library and HMDB database to know the chemical shift of particular metabolites and match the ppm value in chenomx...

30 July 2018 2,924 2 View

Why housekeeping genes vary between control and overexpression group in Quantitative Real time PCR(qPCR) data?

I am using control and overexpression sets (by transfection). while checking for overexpression I can see a sharp decrease in CT value both in housekeeping genes and overexpressed gene. Can...

01 January 1970 9,481 8 View

LCMS based metabolomics by XCMS-METLIN?

I am working in LCMS based metabolomics. I have prepared sample from cancer cell line and acquired spectra in waters xevo g2 xs qtof. As we dont have Progenesis Q software, we have to do it using...

01 January 1970 235 6 View

Is collagen needed for MCF10A 3D culture?

Hi all. I am totally new to this type of experiment- 3D culture. I am planning to study MCF10A cell line in a 3D environment. I am following these two publications as the protocol-...

01 January 1970 8,273 3 View

What should be the gating strategy in flow cytometry with mammalian cultured cell line?

I am doing flow cytometry with the mouse breast cancer cultured cell line and using fluorophore tagged primary antibody (recommended dilution 1:50) against two protein, say A & B. A is a well...

01 January 1970 2,041 9 View

How many MDAMB231 cells to be added for the Matrigel invasion assay?

Hi all, I have to do a Matrigel invasion assay with MDAMB231 cells using Corning BioCoat plates. I have transfection and treatments to do. As far as I have understood from the protocol - I have to...

01 January 1970 3,600 4 View

What type of 96 well plate should be used for fluorescence cell based assay?

Hi all, I have to do Glucose uptake assay using the MCF10A cell line using a fluorescence-based Glucose uptake assay kit (Cayman). Can anyone suggest what type of 96 well plates should be used?...

01 January 1970 4,869 5 View

3D culture with MCF10A cells.

Hi all, I am going to try 3D culture (on top) with MCF10A cells. I am planning to start with matrigel and regular cell culture dishes and then perform confocal microscopy. Can anyone help me with...

01 January 1970 2,818 4 View

How much similarity is allowed in thesis?

Hi all, I am preparing for my thesis submission. When I checked my whole thesis, I got 41% similarity, but when I excluded references, it reduced to 22%. And the major portion (9%) was similar to...

01 January 1970 6,488 6 View

Confusion about ct value of E-Cadherin gene in MCF10A cells

Hi all, I am performing QPCR with the E-cadherin gene and getting ct values around 11-12. I had done the same experiment two years back but back then the ct values ranged around 25-26. Can anybody...

01 January 1970 4,819 3 View

Writing justification for travel grant for attending a seminar

Hi all, I intend to attend a seminar and the selection will be based on an abstract and motivation letter. Can anyone please guide me in writing a comprehensive motivation letter? Another issue...

01 January 1970 886 2 View

Preparation for a Postdoc interview

Hi all, I have been shortlisted for a postdoc interview and asked to give a 10-minute presentation (related to my previous research experience. Please guide me on what should I include and what...

01 January 1970 708 2 View

What are preferable internal and external standards other than TSP in NMR-matabolomics of cancer cells?

Hi all, I am doing NMR-metabolomics in cancer cells. Now, I am facing problem regarding concentration determination of metabolites. I use TSP as internal standard and using TSP concentration other...

01 January 1970 5,372 4 View

Can anyone share a detailed protocol for Nuclear Morphometric Analysis with cell images obtained from confocal Microscopy?

I have cell images from Confocal Microscopy and want to do Nuclear Morphometric Analysis. Can anybody share a detailed protocol to do so? Thanks in advance. Swarnali

01 January 1970 7,148 3 View

Can RNAseq data be analyzed in treated vs control format?

Hi all, I have an RNAseq data and I am trying to analyze it with GSEA software. In GSEA, both the options are available - "Control vs Treated" and "Treated vs Control". Usually, we analyze results...

01 January 1970 4,462 5 View