breast cancer transcriptome

Hello,

I am searching to find the RNAseq for Normal and Tumor (from various classes). Can someone comment where I can download them? I know about TCGA but the normal and tumor is not easy to understand from their data. I appreciate your help

rna-seq

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updated 8.2 years ago by ivanarg2

• written 8.3 years ago by Learner

3 answers

You can use LinkedOmics or cBioPortal.

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written 8.3 years ago by GenoMax

@genomax Thanks for your message. can you please tell me how can I extract the Htseqcount for tumor and normal cases ? here is the link to the transcriptome https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-BRCA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22Transcriptome%20Profiling%22%5D%7D%7D%5D%7D&searchTableTab=cases

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written 8.3 years ago by Learner

What exactly are you trying to do? The two portals I linked allow you to do quick analysis and get processed counts.

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written 8.3 years ago by GenoMax

@genomax I want to obtain the htseq-count for normal samples and tumor samples. This is what I am trying to find

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written 8.3 years ago by Learner

I would download the raw HTseq counts using this listing from the GDC data Portal:

https://portal.gdc.cancer.gov/repository?facetTab=fil...

Mixed among those many files will be normal RNA-seq samples, which (if you're lucky) will be easily identifiable via the TCGA barcode. As these are raw HTseq counts, you will also have to process them yourself. Did you want pre-processed normalised counts?

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written 8.3 years ago by Kevin Blighe

@Kevin Blighe Yes the problem is how to identify Normal from Tumor. the clinical data is very poor for this project. I am just wondering how to identify which one is Normal and which ones are Tumor. I can then use avaiable software for annotation, enrichment analsysi etc etc.

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written 8.3 years ago by Learner

Use the processed data from one of the portals above and save yourself the trouble.

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written 8.3 years ago by GenoMax

@genomax can I assume that Solid Tissue Normal as Normal and Primary Tumor as tumor sample? is that correct?

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written 8.3 years ago by Learner

If you download the data, you'll most likely have directories or file-name as UUIDs. You can obtain the corresponding TCGA barcode using this: Sample names for TCGA data from GDC-legacy archive

With the TCGA barcode, you can infer tumour or normal via the fourth field. See here: Meaning letters in TCGA sample barcode field

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written 8.3 years ago by Kevin Blighe

Use the Xena Browser, selected TCGA BRCA, select "Phenotype" and the "sample_type" will give you tumor and normal data. You can play with the heatmaps as well as download the data.

https://xenabrowser.net/heatmap/

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written 8.2 years ago by ivanarg2