Why do we write t in small letters in tRNA or any other RNA ?

03 March 2017 0 4K Report

Does the small letter in front of every different types of RNA have any significance

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Is there any way to find the biological correlation between miRNA and genes?

We are trying to find the biological correlation between miRNA and certain genes. We found the general correlation through IPA (Ingenuity Pathway Analysis). Thank you for your inputs!

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Please suggest how should i approach for removal of UMI sequence?

I have mi-RNA sequencing data, where my 3 prime adapter is attached with 12 Nucleotide UMI Sequence (in random manner) along with Reverse Transcriptase primer and Universal Adapter Overall...

31 December 2018 691 5 View

How to merge trajectories after extending simulations in desmond?

I found an explanation in Schrodinger's knowledge base but i am not sure how to run the python scripts in Ubuntu. If possible kindly suggest an easy way. Huge Thanks

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Transcription factor binding and expression?

I have a transcription factor protein X and X has a co-activator protein Y. XY bind to the DNA and downstream expression of proteins occur. Now I block the activity of X through inhibitor but dont...

07 August 2018 6,507 7 View

Help with Desmond simulation graph?

Kindly help me interpreting the graph. I am not sure if the ligand is still intact with protein or it has diffused away.

06 July 2018 2,093 6 View

How to carry out membrane protein and peptide simulations?

I want to study the dynamics of ABC transporters along with a peptide molecule which in physiological conditions passes through the transporter. I am clueless how to set the peptide molecule in to...

05 June 2018 6,178 5 View

Help with GROMACS .mdp file parameters?

Hello awesome people, I am new to GROMACS and i have been practicing with different tutorials available online. I successfully ran 1ns simulations. I ran couple of simulations with mdp files as...

01 February 2018 3,665 4 View

Are these normal in Gromacs?

I have following doubts in Gromacs ,and want to know if these things are normal? or i am doing something wrong? 1) The protein is outside the solv box ( picture 1). 2) while i am running...

01 February 2018 7,861 5 View

Software that can find active site itself and dock the protein?

I want to perform protein-protein docking .Please suggest me some software's which can find active site by itself and dock the protein. I have tried HADDOCK but u need to provide active sites in...

08 September 2017 4,725 3 View

Problem with PDB file?

I have docked two proteins using patchdock but i am not able to view the P-P interaction in PIC calculator. I doubt there must be something wrong with the PDB files that i have given as input....

08 September 2017 10,032 8 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

Why Do TDS and EC Increase with Larger Wastewater Volumes, While BOD and COD Decrease?

I have carried out MFC experiments on three different volumes, 50, 500 and 1000 mL of wastewater. Results after MFC treatment shows that TDS and EC are more in larger volumes of water i.e. TDS and...

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Could it be a cell culture contamination?

Hello everyone! I observed in my culture (htert-RPE1 cells) an orange- red particle at the bottom of the dish. It is visible to the naked eye as a very very small red dot. Could it be a...

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RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

Is there any way to quantify bacterial and fungal cells in their mixed culture?

I am working in fungal fermentation of soybean meal and there is bacterial growth in them at times. I am trying to quantify fungal cell counts and bacterial cells; but I haven't been able to do at...

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How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View

Why activated CAR-Jurkat cell could not kill targets?

Previously when I co-coluture anti-CD19(FMC63) CAR-Jurkat with Raji with E:T=5:1, Jurkat can eliminate Raji in 24h. However, when I test another CAR construct, although I can dectect totally CD69...

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E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

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