Bulk transcriptome RNA-Seq dataset of Human breast cancer
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7 months ago

Hi everyone, I'm looking for Bulk transcriptome RNA-Seq datasets of Human breast cancer. But I could not find any datasets that contain all the characteristics that I need for a my favorite dataset. I go through all the ENA, SRA, GEO, TCGA and many more repositories, but still didn't find the right ones. It would be very appreciated if you could help me out in this regard.

Thanks.

RNA-Seq rna-seq dataset human breast cancer • 330 views
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You have not listed the characteristics that you desire.

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Thanks for the reply. Here is the thing that I need to have in a dataset: Bulk+ transcriptome +RNA-Seq datasets +Human breast cancer.

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And how is the TCGA RNA-seq (a method to profile the transcriptome) dataset from human breast cancer patients not fitting to this desire?

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TCGA RNA-seq data does only contain data for Normal and cancer cells but I need more in between, for example; HER2, Ductal cacinoma,.. and so on. Would you please let me know how can I find this dataset? Sorry for my simple questions, actually I dont have background in biology.

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I meant that I need more than tumor and normal samples. Data should encompass other types of samples; such as ; TNBC, ER+, and HER2+.

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Sounds like you are asking for metadata about the samples. This type of data is generally controlled access and you will need to create a proposal to access that.

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Do you mean that I need to contact them directly by "proposal"?

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A principal investigator (your mentor, if you are not a PI yourself) will need to create an eRA commons account and then request access to the controlled data. If your institution does not have access to eRA commons then that would have to be done first (has to be done at administrative level).

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Thank you so your great help. Beside this, is there any repository to get data with those types of samples; (TNBC, ER+, and HER2+...) in breast cancer?

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There are plenty of breast cancer studies that have information on receptor status. I mean, there are literally 1000s of studies. You just need to find a good way to search. Try searching at GEO for a few minutes: https://www.ncbi.nlm.nih.gov/gds

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Thanks. Actually I did alot of search by different types of key words, but couldnt get the desirable result yet

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