what TCGA biospecimen filter should be selected for retrieving "invasive ductal breast carcinoma" data?

Question

[nazaninhoseinkhan]

Dear all,

I want to download RNASeq data related to "invasive ductal carcnoma" breast cancer.

Is there a biospecimen filter that I can use to retrieve specifically invasive ductal carcnoma" breast cancer data from TCGA?

Thank u in advance

Nazanin

[Kevin Blighe]

From where are you aiming to download the data? The abbreviation for the breast invasive ductal carcinoma data is BRCA, and all other abbreviations are listed here: TCGA Study Abbreviations

[nazaninhoseinkhan]

Hi, I am trying to get data from GDC portal.

Thanks for the help, yes I found out that all biospecimens are invasive carcinoma.

I have another question:

• how can I find the protocol of library preparation of my data? I need BRCA data to be prepared by rRNA depletion method.

[Kevin Blighe]

Here is a configuration for all BRCA rRNA-depleted HTseq RNA-seq raw counts: https://portal.gdc.cancer.gov/repository?facetTab=...

If there are non-rRNA-depleted samples, they will be listed as Total RNA-seq in the GDC. For example, here are the total RNA BRCA RNA-seq samplers, at the GDC Legacy Archive: https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7...

[nazaninhoseinkhan]

Thank u so much

I am really expressed by your expertise in different fields of bioinformatics

[Kevin Blighe]

No problem, my friend. Please do not hesitate to come back for more advice in the future.