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Questions related to Bioinformatics
I am looking for a buffer solution to preserve the DNA in dissociated muscle cells at room temperature (because I need to transport them at room temperature). The cells do not have to be viable, I...
11 January 2023 5,222 2 View
Hello, I have band of my negative control. I am sure there is no contamination. I used new everything, sterile and change my gloves 5 times. I did negative control mix separately my samples. My...
03 January 2023 6,712 10 View
I am working on immobilization of peroxidase on magnetic nanoparticles, I want to study the influence of immobilization on pH, Temperature and kinetics of the enzyme. How to do so given that the...
02 January 2023 8,107 4 View
Can someone please list the analysis that needs to be performed to understand and compare the mechanism of a protein in its native and inhibitor-bound state? (NOTE: Not the interaction between...
25 December 2022 1,332 3 View
Kit used: MN - Nucleospin Gel and PCR cleanup kit
21 December 2022 3,664 3 View
Why is phenol-chloroform used in nucleic acid extraction and not any other solvent ? There are many solvents, but why only phenol-chloroform is used...
05 December 2022 4,205 2 View
Hi, I am using the same DNA template to run two 7kb PCR experiments with the same cycling conditions simultaneously. The only difference between the two experiments is the primer pair. One result...
03 December 2022 4,836 7 View
Hello, I am currently docking my ligand with a target and getting a positive binding energy in AutoDock while Vina gave expected negative value. What can be wrong with docking in AutoDock? Thank...
01 December 2022 8,068 4 View
Hey, I'm trying to optimize a molecule by using GAMESS US with solvent (water, PCM) while constraining Cs symmetry. When I add solvent the symmetry changes (C1) even though the GAMESS acknowledges...
22 November 2022 3,642 1 View
Hi, I'm looking for a product recommendation. I want to seal microplates containing bacteria for an overnight growth curve at 30-37 degrees C. The job of the seal is to keep moisture from escaping...
06 November 2022 289 3 View
Hello everyone I had a kinase+ATP-Mg complex. I ran MS simulation for 100 ns. via GROMACS and CHARMM36. The system is stable (backbone RMSD is and reach plateau before 20 ns.). When I used...
03 November 2022 3,770 11 View
I'm working with swabs collected from fish mucus to look for microbes but I am not sure about the right bead beating time and the number of cycles. Thank you!
21 September 2022 5,981 1 View
Does anyone know if Illumina adapter sequences have changed for NovaSeq 6000? I tried using the sequences described for HiSeq 2500 / TruSeq for trimming my raw data and it didn't work well for...
05 September 2022 8,576 7 View
Hi all, I want to download some reference microbiome data from NCBI sequence Read Archive (SRA). I previously used fasterq-dump or fastq-dump to download the data, and the data were used to be...
08 August 2022 7,849 1 View
Hi everyone, Here are the nanodrop reading values for DNA concentration after the chromatin de-crosslinking step followed by elution with 20 uL elution buffer. Sample ng/uL ...
23 June 2022 6,150 0 View
Hi everyone, I have the reagents to culture A549 Cells but don't know what volumes to use. I have DMEM, FBS, Pen/Strep, Amphotericin B. for growth. Could anyone advise me on volumes...
23 May 2022 903 1 View
Hi, I'm running an immunoprecipitation experiment, trying to pulldown actin from some RAW 264.7 cell homogenates. I ran a Western blot with a 1:5000 dilution of biotinylated anti-actin...
03 May 2022 1,323 0 View
I was wondering on the preparation of lyticase (sigma L2524-10KU). I could not find specifically on to prepare the stock solution to use in pulse field gel electrophoresis. Does any one know...
08 April 2022 1,463 0 View
I have to add protease inhibitor and phosphatase inhibitor during cell lysis in a six well plate. How can i calculate the amount of protease and phosphatase inhibitor amount ?
08 March 2022 303 1 View
For my project I need to measure the OD600 of my bacterial cultures over time in 96 wells plates, but due to technical reasons my plates must be sealed. Therefore, I need a seal that allow gas...
07 March 2022 6,165 0 View
Hello, I am struggling to interpret couple of splice site mutations I have encountered and I would like to ask if there is a way to predict the outcome of a given splice site mutation (does it...
02 March 2022 7,969 1 View
Dear All, I am trying to simulate Fe hydrogenases. however, I am unable to parametrise the FeS clusters. There are 4 different types : Fe3S4, Fe4S3, Fe4S4 and Fe attached to Carbon and Nitrogen....
08 February 2022 8,636 3 View
I have the problem, like several other people before, that large proteins get lost during electrophoresis in the SDS PAGE gel. All protein bands below 80 kDa are perfectly separated as usual, the...
18 October 2021 6,038 8 View
Hi, I am looking for a tool (an online/free tool is better) to filter potentially problematic substructures. I found an online tool called "PAINS Remover" (https://www.cbligand.org/PAINS/) but...
12 October 2021 2,171 0 View