targeted bam file from database for breast cancer

Question

[mittu1602]

Hello all,

Could anyone help me any database or website from where I can download one .bam file with following criteria:

1. Breast cancer (ERBB2 positive)
2. Targeted sequencing data

Thank you

Answer 1

[Kevin Blighe]

Hey, you could download data for the ERBB2/HER2 positive breast cancer cell-line, SKBR3:

Whole genome

https://www.ncbi.nlm.nih.gov/sra/SRX750519[accn]

Exome

https://www.ncbi.nlm.nih.gov/sra/SRX317807[accn]

I could not find a targeted sequencing project looking at just ERBB2/HER2 (I have that data myself but it's private/not openly available).

I presume that you are aiming to look at copy number of ERBB2 from the mapped reads?

Another ERBB2/HER2 positive breast cancer cell-line is MDA-MB-453 - you could also search the same website for data on that. There is a lot of other data on SKBR3, mainly ChIP-seq data from what I saw.

Kevin

[mittu1602]

Thank you for your response. Yes I am aiming to look at copy number of ERBB2 from the mapped reads. This data should help me with my work.