Cancer cell line WGS

Question

[de.subhajyoti]

I am looking for WGS data (fastq or bam files) for some of the commonly used cancer cell lines. I believe COSMIC Cancer cell Line Project has processed mutation calls for some of the cancer cell lines, and the cgHub has WGS data for only 3 cancer cell lines. But I am after the raw fastq or bam files for 15-20 common cancer cell lines. Any suggestion will be greatly appreciated.

Answer 1

[alolex]

Have you checked ENCODE? Search for "whole-genome" here

It looks like they have fastq files for GM12878 and H1-hESC, but you may already have those from cgHub.

[de.subhajyoti]

GM12878 and H1-hESC are not cancer cell lines. But WGS for K562, which is a cancer cell line (and 2 other cancer cell lines), seems to be available from the cgHub.

[wqshi.nudt]

I want the whole genome sequencing (WGS) of K562 and H1-hESC for my project. Did you find K562 at cgHub? I tried, but failed.

ENCODE project just did the whole-genome shotgun bisulfite sequencing, and this is different from WGS.

[de.subhajyoti]

This is the search result from CGHub (columns transformed into rows below)

CCLE
CCLE-K-562-DNA-08
LCLL
CELL
WGS
BI
ILLUMINA
HG19_Broad_variant
210.79 GB
c72531e9-0e79-91c5-e040-ad451e411a96
2013-05-16
Live