Question: extracting gene expression for cardiomyocyte tissue
0
gravatar for nfs.falsafi
12 days ago by
nfs.falsafi20
nfs.falsafi20 wrote:

Hi all,

I have a set of microarray data included embryonic fibroblast, induced cardiomyocyte and cardiomyocyte from tissue. as we all know, to extracting gene expression of induced cardiomyocyte, we need to consider a set of fibroblast as a control and the iCM for treatment. is it correct to extracting gene expression for cardiomyocyte tissue by using fibroblast as control and cardiomyocyte tissue set as a treatment? or is there another way?

ADD COMMENTlink written 12 days ago by nfs.falsafi20

What is your experimental design? What are you trying to show? The changes caused by the induction? I don't have any idea about cardiomyocyte development, but why use the fibroblasts rather than the cardiomyocytes from tissue as the control?

ADD REPLYlink written 12 days ago by jared.andrews071.3k

you know, I try to extract gene expression of cardiomyocyte tissue to show how similar are iCM and CM expression. Finally, we can conclude whether our iCM is similar to cardiomyocyte or not. if it is similar then our induction is pretty good.

ADD REPLYlink modified 12 days ago • written 12 days ago by nfs.falsafi20

Wouldn't it make sense to do the analysis between those two sets to show there are few differentially expressed genes between them then?

ADD REPLYlink written 12 days ago by jared.andrews071.3k

what is your suggestion to compare induced cardiomyocyte and cardiomycyte gene expression? I want to show them as a heat map but before this, a gene expression of cardiac is needed.

ADD REPLYlink written 12 days ago by nfs.falsafi20
1

limma is kind of standard of microarray analyses. You can make heatmaps with any number of packages. I guess you could also compare each to fibroblasts, then compare the resulting lists of genes to each other to show that they match up well.

ADD REPLYlink written 12 days ago by jared.andrews071.3k

You mean I compare iCM and CM with fibroblast to get reseanable gene expression?

ADD REPLYlink written 12 days ago by nfs.falsafi20
1

Yes, then compare the resulting lists of differentially expressed genes between iCM/fibroblast and CM/fibroblasts to show that they have good overlap, i.e. that your induced CMs closely match normal CMs.

ADD REPLYlink written 11 days ago by jared.andrews071.3k
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