Question: Cancer cell line WGS
2
gravatar for de.subhajyoti
4.1 years ago by
United States
de.subhajyoti20 wrote:

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.

sequencing next-gen • 2.9k views
ADD COMMENTlink modified 4.1 years ago by alolex900 • written 4.1 years ago by de.subhajyoti20
1
gravatar for alolex
4.1 years ago by
alolex900
United States
alolex900 wrote:

Have you checked ENCODE?  Search for "whole-genome" here: https://www.encodeproject.org/experiments

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

 

ADD COMMENTlink written 4.1 years ago by alolex900

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. 

ADD REPLYlink written 4.1 years ago by de.subhajyoti20
1

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.

 

ADD REPLYlink written 3.8 years ago by wqshi.nudt20

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

 

ADD REPLYlink written 3.8 years ago by de.subhajyoti20
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