gene expression values in CCLE miRNA datasets

Q&A
1

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

2

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.

Thanks,
Simone

3

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