Place to Acquire Bulk RNA-seq Cancer Datasets with Survival and Followup information

Question

[sizetype_pacher]

Hi all,

I am currently looking to validate a pipeline I have created that involves using Cox models. I have used TCGA bulk RNA-Seq-datasets. Unfortunately, I also need to use another data source besides TCGA to complete the project. I am having difficulty finding cancer datasets that meet the following requirements:

1. Normalized (TPM/FPKM) bulk rna-sequencing data from various cancers
2. Contain vital status (e.g. alive or dead)
3. Contain followup information (e.g. how many days did a patient live during the study)
4. Dataset that is not from TCGA
5. Contain patient information

I have been able to get close finding datasets that contain patient information, normalized sequencing data, and survival status that is not from TCGA, but it lacks followup time which is a requirement for survival analysis (Cox models).

Thanks in advance!

[Dan]

You can try cBioportal https://www.cbioportal.org/ which has patient information.

Answer 1

[qiz218591]

How about using the data from the GEO database, you will surely find the datasets from there according to your requirement.