Aravind Tallam

10 Questions 27 Answers 0 Followers

Questions related from Aravind Tallam

Is there a company which can prepare reporter plasmids for a Luciferase assay?

I would like to do Luciferase reporter assay to identify regulatory sequences/sites in the promoter region of my gene of interest (both in human and mouse). I am aware that this experiment...

26 April 2014 4,754 3 View

Which network inference tools give directionality and sign for intercations from gene expression data?

I am using different network inference tools like GENIE3 and TIGRESS which give directionality but not the sign of interaction (activation/inhibition). Some tools like Inferelator give it if we...

18 April 2014 4,432 1 View

Can anyone suggest a protocol for siRNA/shRNA inhibition in human primary macrophages or is there a human primary macrophage cell line?

I have been working with Human primary macrophages (differentiated from monocytes isolated from blood) and the experiments done to date with siRNA and shRNA (Nucleofection) in these cells were...

29 November 2013 2,908 0 View

How can we know whether a gene is a Transcription factor or not?

I have differentially expressed genes from my microarray data and i would like to know if there are any knowledge sources/tools with the collection of all known Transcription factors from...

03 September 2013 8,092 6 View

How to deduce important paths between two given nodes in a network?

I have a network with 500 nodes and 400 edges. Iam interested in the pathways between 2 nodes and for that i have calculated all the shortest paths between that 2 nodes. To test experimentally, i...

30 August 2013 573 4 View

How to combine Network predictions from literature and Network inference methods?

Using GEO data and network inference methods (GRN), I have got relationships between genes from each GRN method (example, GENIE3, CLR, LASSO). For specific genes which I am interested, I have got...

21 March 2013 6,058 3 View

How to identify significant differentially expressed genes from samples with out replicates?

I downloaded a dataset from GEO (GSE1906) and they have only 1 sample (I mean with out any replicates/triplicates) per condition and their data files contain the measure of the abundance of a...

21 March 2013 2,414 5 View

How to interpret the SOFT files of a microarray experiment?

As you might know that some of the datasets in GEO will contain the data in SOFT formatted files instead of CEL files which contains the abundance of the transcripts. Do we need to consider these...

21 February 2013 7,335 8 View

Serum free medium for monocyte-macrophage differentiation

For the differentiation of human primary monocytes to macrophages, I use human serum added to RPMI. Due to some problems with the human serum, the cells isolated from a lot of blood samples...

15 October 2012 9,660 11 View

Are there any research protocols or commercial kits available for isolating monocytes from mouse blood and differentiating them into macrophages?

I will be sacrificing mice and will extract blood by cardiac puncture. I need to isolate monocytes and differentiate them into macrophages. I found some papers but they modify the protocol...

01 March 2012 3,021 12 View