human RNAseq data from negative Controls (not cancer)

[JUAN MANUEL LUQUE SANCHEZ]

Dear Srs.:


I would like to ask you,please,if CBioportal has files of human
RNAseq data from negative Controls (not cancer),for a large number of
samples/patients.Or where can I download it?.

Thank you very much for your help.
Best regards

Juan M. Luque

[Tali Mazor]

Hi Juan,

cBioPortal does not have RNA-seq data from non-cancer samples. Other resources do have non-cancer RNA-seq data available, for example GDC: https://gdc.cancer.gov/about-data/publications/pancanatlas

-Tali

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[JUAN MANUEL LUQUE SANCHEZ]

Hi Tali,

Thank you very much for your answer.I have seen this in your web(in FAQs):

Is there any normal RNA-seq data in cBioPortal?

We have RNASeqV2 mRNA expression data for normal samples of 16 TCGA
PanCan Atlas Cohorts. The data was curated from GDC, and can be
downloaded from our Datahub or Data Set page. This data is not
directly queriable in portal; they are only used as reference data for
calculating the "relavtive to normal expression z-score" profile.
Example: ERBB2 expression z-scores relative to normal expression.

Looking the file download for example :
data_mrna_seq_V2_rsam_zscores_ref_all_samples.txt (for a type of
cancer) ,¿this file are the negative controls (non-cancer) of this
cohort /study of this type of cancer?

Thank you very much for your help.

Juan M. Luque
Tali Mazor <tma...@ds.dfci.harvard.edu> escribió:

[Tali Mazor]

Hi Juan,

The file you mentioned is z-scores for tumor samples. The RNA seq data for normal samples is in a folder called 'normals' within each study, for example: https://github.com/cBioPortal/datahub/tree/master/public/chol_tcga_pan_can_atlas_2018/normals

-Tali

[JUAN MANUEL LUQUE SANCHEZ]

Hi Tali,

Thank you very much.I see in this folder (normals) 1 file with RNAseq
data from 10 normal samples.That'ś right?.Are there more than 10
normal samples or they are only 10 normal samples?

Thank you for your help.
Best regards.

[Nikolaus Schultz]

Hi Juan,

That is correct, there are only 10 normals for this study.

Niki.

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