Question: what TCGA biospecimen filter should be selected for retrieving "invasive ductal breast carcinoma" data?
0
gravatar for nazaninhoseinkhan
19 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

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

ADD COMMENTlink written 19 months ago by nazaninhoseinkhan390
1

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

ADD REPLYlink written 19 months ago by Kevin Blighe54k

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.
ADD REPLYlink written 19 months ago by nazaninhoseinkhan390
1

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...

ADD REPLYlink written 19 months ago by Kevin Blighe54k

Thank u so much

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

ADD REPLYlink written 19 months ago by nazaninhoseinkhan390

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

ADD REPLYlink written 19 months ago by Kevin Blighe54k
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