We haven't used mammalian cells before, so we need some help. So, for our experiments we want to know for our gene of interest specifically, how may copies are present and what the sequence is (i.e. which SNPs are in each copy). Does anyone know the best way to get this info? Do we need to do high throughput sequencing of the DNA ourselves, is there a database somewhere, or is there a company that contracts out this type of service?
Interesting question. If you are working with a mouse cell line, you might be able to find the information of the genotype of the mouse strain from which it was isolated on the ATCC (American Type Culture Collection) website. However, even if this information is available, it will only partially answer your question since many established cell lines are aneuploid or have other chromosomal anomalies that will affect gene copy numbers.
Thus in all likelihood, you would have to invest in directly testing copy number variations, and gene sequencing to assess SNPs. Or you could try to immortalize a primary cell type of known genotype using hTERT. In the end, this approach might be simpler, if you have access to tissues from individuals with the specific genotypes of interest.
If you happen to be using a cancer cell line, you might find the following website useful:
http://cancer.sanger.ac.uk/cancergenome/projects/cell_lines/about.html
I have not seen a similar database for genotype information on "normal" mammalian cell lines, however (although it may exist).
Or just check the cbio Portal (http://www.cbioportal.org/) and select the Cancer Cell Line Encyclopedia as "study". Here you can find mutations for many genes in several hundreds of cancer cell lines. In terms of mutations this is the pretty best data set for your question I am aware of.
I would first use the direct sequencing method to find a SNP. Then I will verify using assy by design. Or If you think your SNP is common KNOWN SNP you can use affimatrix or Roche chips.
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