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U2OS cell line reference genome

I need some help. I am not being able to find U2OS cell line reference genome. There are some assemblies in NCBI SRA, but I am unable to find any site where I can get the reference sequence. Also, in case this is unavailable, how can I create a reference of my own?

reference alignment
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written by anubratadas • anubratadas

Hi @Arup Ghosh, thank you so much for advice. I am looking at telomeres, and U2OS cell lines have long telomeres, which I am unable to find in the T2TChM13 reference genome. I agree that since it is telomeric, the sequence should be same. I expanded the ends of chromosomes, with telomeric sequence and used it as the new reference, but in IGV, I don't see the reads mapping to the telomeric region aligning with these extended reference sequence too. these reads are always soft-clipped. Hence, I suspect, this might be due to TVR (variant repeats) in the telomeres of U2OS. Hence, I was thinking if I could get an U2OS genome. Thanks once again

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written by anubratadas • anubratadas

Telomeres are repetitive and therefore mostly unmappable for short (any some long) read technologies. It is very unusual to use cellline-specific reference genomes, in part because there are thousands of clones of this cellline around and each of them have different variant profiles.

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written by ATpoint ATpoint

ATpoint, many thanks for this insight. I now know that I should not attempt creating any U2OS specific reference.

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written by anubratadas • anubratadas

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