Hello, I have chosen some cell lines on the bases of information available on cancer cell line encyclopedia but while my experiments I am not getting the same results . Can anyone tell how do they get the copy number variation data? Is it whole genome sequencing based or else is it possible to get some different results what has been reported in this database. please help....
Dear Heena,
Try to get the same information from Oncomine database and compare.
Best,
Mannan
For CNV check cosmic
http://cancer.sanger.ac.uk/cosmic/help/cnv/overview
Check whether your cell line is there in their CNV cell line project
http://cancer.sanger.ac.uk/cell_lines/
Best
Hello,
Thanks for your replies to my query. I checked the COSMIC database but my cell line study is not available in it.
and with Oncomine I have registered to it but they hadn't send me the user ID yet.
If you have some other sources please tell me....
Another place to look for is cell miner from NCI the cell types they have analyzed is listed here :
https://discover.nci.nih.gov/cellminer/metadata.do
Also in CCLE what method did they use? You should be able to get that information. Are you not able to reproduce that data using same methods?
Best
Hello mam,
Thank you for suggestion. I have also checked through cell miner but my cell line data is not available in it.
CCLE data is based on the results of affymatrix snp 6.0 , I am not using same method. They have reported homozygous deletion of the gene but I am getting its expression in RT-PCR.
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