method for isolating/separating the y chromosome? - (Nov/29/2007 )
I am trying to figure out a way to separate the Y chromosome from the rest of the dna and mtdna. Does anyone know of any methods? I've found a bit of information about "conversion technology" which is being used to separate autosomal chromosomes so haploid chromosomes can be sequenced/typed. That's not exactly what I'm looking for.
I haven't found anything on separating the Y. In a species that I'm studying I'd really like to have that completely separate.
what do you actually mean? Do you want to isolate the Y chromosome? or do you want to isolate DNA from the Y chromsome. What do you want to do with the chromosome once you have it?
I want to isolate the Y chromosome itself. I'm just looking at the feasibility of sequencing the whole y chromosome by separating it from the other chromosomes first. the y chromosome hasn't been sequenced in the species that i'm studying and i'm just trying to get some idea of methods available (and cost and time of course).
Flow cytometry to isolate chromosomes. But it seems like there is special flow cyto requirements for sorting chromosomes and thus only specialized labs can do this. (We're trying to see if it can be done on our "ordinary" FACS Aria next week).
There is also a paper and patent on using biotinylated probes to pull down entire chromosomes.
Along the same line, check out the 3 papers (Nature Methods, Oct or Nov) on using capture probes on Nimblegen microarrays to enrich for sequences of interest prior to sequencing.
maybe you could fish it out with a y chromosome specific probe (attached to a magnetic bead?). that way you won't have to wait for prophase to see the chromosomes.
I think it is probably best to actually trap all the cells at metaphase and lyse them at that point. I think there might be severe sheering problems should uncondensed chromatin be manipulated.