# gene expression values in CCLE miRNA datasets

**URL:** <https://forum.depmap.org/t/gene-expression-values-in-ccle-mirna-datasets/3309>\
**Category:** Q&A\
**Created:** [June 3, 2024, 2:01am UTC](https://forum.depmap.org/t/gene-expression-values-in-ccle-mirna-datasets/3309 "2024-06-03T02:01:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Shang\_Su](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/shang_su/32/979_2.png) [@Shang\_Su](https://forum.depmap.org/u/Shang_Su)\
**Post date:** [June 3, 2024, 2:01am UTC](https://forum.depmap.org/t/gene-expression-values-in-ccle-mirna-datasets/3309/1 "2024-06-03T02:01:39Z")

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Hi folks!

I am trying to explore the correlation among a protein-coding gene, a LncRNA, and a microRNA among lung cancer cell lines. CCLE2019 datasets seem to suit my needs. But I got a little uncertain which dataset I should use.

I saw RNAseq\_genes\_rpkm and RNAseq\_genes\_tpm for regular RNAseq.  
I also saw miRNA\_MIMAT and miRNA\_20181103.gct.

May I ask if the MIMAT and 20181103.gct are interchangable dataset with same normalization method? Is it rpkm or tpm annotated?

Thanks,  
Shang

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [June 3, 2024, 6:00pm UTC](https://forum.depmap.org/t/gene-expression-values-in-ccle-mirna-datasets/3309/2 "2024-06-03T18:00:33Z")

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Hi Shang,

I’m not personally familiar with the data generation process for these but the file description for CCLE\_miRNA\_MIMAT.csv says “The same CCLE miRNA expression data as CCLE\_miRNA\_20181103.gct except the IDs have been mapped to MIMAT IDs based on miRbase”. For details on data normalization, please refer to the “Nanostring data quality control and normalization” section in the [CCLE paper](https://www.nature.com/articles/s41586-019-1186-3).

Thanks,  
Simone

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**Author:** ![Shang\_Su](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/shang_su/32/979_2.png) [@Shang\_Su](https://forum.depmap.org/u/Shang_Su)\
**Post date:** [June 12, 2024, 8:08pm UTC](https://forum.depmap.org/t/gene-expression-values-in-ccle-mirna-datasets/3309/3 "2024-06-12T20:08:52Z")

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Thanks Simz for the information. I missed that probably due to different access manner.