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Questions related from Pratik Ramjivan Shriwas
Dear all, I am trying to learn GSEA software tool and curently working on GEO dataset; GSE41586. When i downloaded the data and extracted it, I found many genes have duplicates as well as many...
09 February 2025 9,519 2 View
Schrödinger is one of the most prominent software for molecular docking. Is MOE also reliable for ligand docking. regards, Pratik
07 September 2023 910 3 View
Hi, I am trying to develop a method for CYP2C9 inhibition by some compounds. I wanted to use flourescent based assays for this. So, I decided to use Dibenzylfluorescein (DBF) for this assay. I...
12 September 2021 1,419 3 View
Hi, I am trying to perform enzyme kinetics studies using Benzoxy resorufin ether as a fluorescent substrate. CYP2B6 metabolized this substrate to resorufin, whose fluorescence can be measure at EX...
23 August 2021 5,211 4 View
Hi, I have input data in Metaboanalyst in MS peaks to pathway module. I was able to find the graph as attached (input figure 1). I also generated the report. But I am not sure how would I get a...
15 January 2020 2,820 2 View
Hi, I have input data in metaboanalyst in MS peaks to pathway module. I was able to find the graph as attached (input figure 1). I also generated the report. But I am not sure how would I get a...
11 January 2020 7,375 0 View
I am trying to model a protein based on its homology. The two share 65% sequence identity. Is that good enough for basic modeling or should I opt for advanced modeling using Modeller? Btw, The...
02 March 2019 7,272 8 View
Hi, I generated a crispr ko cell line. The protein was more than 90% knocked out. But, now after several months od thawing and repassaging,the protein seems to comeback. I plan to do a grloth...
12 January 2019 4,101 9 View
I tried to transfer today and found that the membrane (membrane 1) looked like this after ponceau S staining. Two days ago, I transferred two membranes together in the same cassette and found...
24 December 2018 2,907 6 View
I just performed LC-MS/MS analysis. I have got a file with m/z, retention time, fragment score, etc. I want to know how can I do a pathway analysis and identify compounds? Which softwares...
07 December 2018 4,505 16 View
Hi, I am having problem using chimera for receptor-ligand docking. There are two issues. 1. If I have a protein can I generate a pdb file for its homolog (the sequence of which is known). 2. If...
01 July 2018 7,278 5 View
I want to optimize my cell transfection study using puromycin selection in A549 cells. I have used 0.5, 1, 1.5, 2, 2.5 and 3 ug/ml of puromycin. I found out that all cells are killed in 1.5 and...
27 June 2018 8,466 4 View
Hi, Guys, I performed cell cycle analysis using PI staining recently. The problem is the compound I am working should lead to cell cycle arrest and the data suggests that. But, this is not...
05 June 2018 6,290 3 View
I am attaching images of my cells after DAPI staining. Please tell me if they are contaminated. The problem is when I keep exposure time on microscope as 600 ms, I do not see small dots but when I...
23 May 2018 513 3 View
Hi, I have recently performed metabolomics. But, I am finding some difficulty. I have encountered PEG contamination. Although, I am using MZmine software and able to SCREEN out contaminants. I...
02 May 2018 1,820 7 View
Hi, I performed Metabolomics analysis on my sample. I saw some PEG contamination but also I saw lots of metabolites. I have a control sample and treated sample. I have extracted the data...
06 April 2018 9,441 4 View
Hi, I am attaching flourscence staining images with DAPI of my A549 cells. A1 and B1 are different vials. Please let me know if my cells are contaminated. I have literally wasted months...
19 March 2018 7,273 4 View
Hi, I want to isotopically label my compound and study it. Can someone suggest some companies for this. How much is the usual cost and how much doe sit take (based on previous experience)?
29 January 2018 6,484 3 View
I am using fluorescence microscopy to detect apoptosis and necrosis. I use cancer cells and treat it with anticancer compounds. I am using Annexin V (apoptosis) and Propidium iodide (1 mg/ml ) for...
18 December 2017 9,970 5 View
Hi, I plan to do metabolic profiling of cancer cells. For that, I am supposed to perform the following steps 1. Cell lysis 2. Cyroextraction using methanol and water 3. Vaccum evaporation and...
17 September 2017 2,061 4 View
Hi, I have recently purchased HOP92 cell line from NCI. I wanted to know what is the correct culture media for it. The document from NCI repository says: GROWTH MEDIUM: RPMI...
07 September 2017 2,445 1 View
Hi, I want to generate knockout cell lines by knocking out three genes. I wanted to use sgRNA/tracrRNA and Cas9 co-transfection for the same. CAn someone suggest the companies from which to buy...
06 July 2017 4,486 6 View
ROS, I know at low levels promote tumor growth and moderate levels active HIF1A which result in increase in glucose uptake. But at high levels, lead to cell death via DNA damage or apoptosis. So...
07 June 2017 1,511 2 View
Hi, I want to test the efficacy of our anticancer compounds in 3D spheroid cell culture. We are working on A549 lung cancer cells. Can someone suggest a protocol, publication or some other...
24 May 2017 2,053 1 View
Hi... I want to generate a Cripsr based cell line which has three gene knockouts. Can someone share thr protocol with methods for validation at each and every step. Its like a cell expresses 4...
21 May 2017 9,980 7 View
Hi, I want to determine the mechanism of programmed cell death in cancer cells due to our compound. I want to study necrosis but unable to find any kit. Trypan blue staining is recommended for...
19 May 2017 6,497 5 View
I am performing an experiment to study cell cycle analysis after anticancer compound treatment. I am planning to use flow cytometry. Can someone suggest a protocol for this. I just want to study...
12 May 2017 6,851 9 View
I am working on a compound and studying its cytotoxicity on cancer cells. I want to know if necrosis is the cause of cell death. I would be grateful if someone can suggest how can I study...
08 May 2017 5,708 5 View
Hi, I am trying to study the synergistic effects with our compound and other anticancer drugs. I have been successful with compounds such as Sunitinib, Paclitaxel and Pazopanib but I am failing...
05 May 2017 10,076 2 View
Hi, I want to test the synergistic effects between my compound and Cisplatin/Bromopyruvate in A549 non-small lung cancer cells. I tried dissolving Cisplatin/Bromopyruvate in DMSO but the results...
20 January 2017 5,970 12 View
Hi, I have performed several MTT assays but find lots of variations in my data. I am not sure what is wrong with my technique. I have used glucose uptake assay,ATP assay but the variations are...
01 October 2016 1,106 2 View
I have some compounds which are supposedly glucose transport inhibitors on cancer cells A549 and H1299. I have worked with almost 20 such compounds. I have used concentration of 30 μM for glucose...
30 June 2016 10,014 9 View
Hi, I was performing MTT assay in my lab hood. Accidentally, I did not turn off germicidal lamp (UV-C 254 nm) in the hood and I worked for about 25 minutes. I was wearing latex gloves and my hands...
13 May 2016 8,907 3 View
