Entering edit mode
11.4 years ago
satish.nair
•
0
Hi,
I would like to know whether we have a synthetic data available for Human single cell which I can use to identify the relation between the cells using different phylogenetic tree finding programs?
If I am ablle to find the synthetic data then I would be able to use that as a control to check the efiiciency and accuracy of my pipeline in finding the phylogenetic tree.
I would like to get the synthetic data in which I know the exact relation between the cells and everything should be of the same organism. That is I am trying to find the relation between the cells of the same organism..
Thanks in advance
Satish
What sort of data are you looking for? Micro-array, RNAseq, ChIP-seq, DNA-seq?
Are you looking for relationships between different cells WITHIN a tissue, or cells sampled from DIFFERENT tissues/cell lineages?
Can you also comment by what you mean when you say phylogenetics of synthetic data? I'm completely confused.
Thirding the request for more clarity. What do you mean by synthetic data for a single human cell? What type of data are you looking for? What are you intending to compare in order to construct a phylogenetic tree? Normally in humans if we are talking populations of cells we are usually looking at cancer cells and building trees to see how they are differentiating. Is that the sort of analysis you are doing?
Hi sorry for the late reply. I am dealing with the NGS data from ILLUMINA. I am trying to find out a pipeline which uses the input as NGS data and finally gives out a tree of the different single samples that I am using as the input. These single cells are from the same tissue.
Actuallly I have seen a paper in which they have used the cancer cells to prepare a tree. For my case : 1) I need data which we already know how they are related to each other. 2) They means different SINGLE CELLS of the same tissue in HUMANS. 3) The data should be in fasta format. 4) So I can generate the NGS reads for them and use my pipeline and finally I will get the relation between the cells(PHYLOGENETIC ANALYSIS) 5) If I already know how these single cells are related then I can check whether my pipeline is able to find the relation accurately or not. 6) I am trying to find how the cells in our body are related because all these cells came from a common root.
Can you provide us with a link to said "paper in which they used the cancer cells to prepare a tree"? I'm still confused so I want to see what exact you are talking about.
I'm not sure such data exists. It would require something like seeding a single cancer cell and sampling as differentiation occurs, or starting with an iPS cell and inducing multiple differentiations. You may need to go about other ways of testing your pipeline.
http://www.cell.com/retrieve/pii/S0092867412002255
So, what I have been hoping to get out of you is more details here. You want to construct a phylogenetic tree, but you don't do that out of "a single human cancer cell", you have genetic data. What gene are you studying, what type of genetic data do you have (or would like to have) and what is your research question? What is your optimal data to test your pipeline?