I want to identify clones from a cell line. I need to know the techniques to identify if the cells I separate are the same or different clones.
this depends on what the differences are between your subclones.
on what basis did you descide to subclone your culture?
histological differences? then you might expect mutations or gene expression differences, which would require sequencing or gene expression analyses.
but if you expect genomic instability for example, something like FACS analysis of DNA content (simple PI staining) would be a good start to see whether some subclones have gained or lost chromosomes compared to the others
I usually verify that the well has only one cell immediately after plating and mark the well to make sure the cells growing in that well are in fact single cell derived. I mark several such wells with single cells. Once they proliferate enough, you may screen for desired qualities to choose the clones.
I agree with the comments. You can also get clones by a soft-agar assay and then isolate colonies and expand them in culture, that's another way to get clones for further analysis.
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