How to do median and quantile normalization of microarray data in GEO which does not have .CEL files?

I want to normalize the GSE data which is in .txt format i.e non-normalized. How to do median and quantile normalization of this .txt file using R? Your help is appreciated Thanks

01 February 2017 9,990 0 View

How to calculate number of Calcium ions during MD simulation?

I want to add 1mM calcium ions inside my protein simulation box after knowing the number of water molecules in water box. How to calculate the calcium ions? What are the steps in GROMACS to follow...

07 August 2016 8,983 4 View

Is 20ns simulation enough to study 317 amino acid length protein in GROMACS?

My protein is a cysteine protease of 317 aa with a single point mutation. I want to simulate the mutated structure. What should be the time length ?

06 July 2016 3,427 8 View

Next Generation Sequencing Training?

There is a highly recognized company in the field of Life Sciences/ Bioinformatics- Shodhaka, which is planning to organize high throughput training in Next Generation Sequencing, but they need a...

06 July 2016 3,066 0 View

MD Simulation in GROMACS 5.0 at a specific pH?

I'm working on a protein which is active at pH =5. I want to simulate this protein with a mutation at pH 5. How to give this parameter?

06 July 2016 8,339 4 View

Is there a database of pre-validated Real-Time PCR primers?

I want a database where experimentally validated Q-PCR PRIMERS are available . I am using SYBR Green for real-time PCR. Waiting for your valuable answers.

02 March 2015 4,654 2 View

Is it right to design primers for Real-Time PCR (SYBR-Green) by using coding the sequence as the template?

I downloaded the Coding Sequence s from NCBI and designed primers using Primer-BLAST (NCBI)

02 March 2015 5,750 5 View

Which is the most validated gene to be used as a control in Q-PCR ?

My Experiment sample is pancreatic tissue. Please help me in deciding the control gene to be analysed by Q-PCR.

02 March 2015 7,577 19 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

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02 March 2021 3,060 3 View

Issues with Permeabilization during Flow Cytometry?

Hello Everyone. Currently I am working to characterize macrophages in the myocardium after ischemia-reperfusion injury in rats. Due to the low total cell number isolated from rat hearts I can...

01 March 2021 3,867 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 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

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 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

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

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28 February 2021 9,936 2 View

Has anyone had luck using cell lines other than HEK 293 (such as COS1) to package lentivirus?

I am looking to package lentivirus in endothelial cells but I am opposed to using 293 cells due to personal ethics regarding the source. I have done some reading and saw that COS1, COS7, & CHO...

25 February 2021 3,030 1 View