miRNA and transcripts in 21Q3

Q&A
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1

Hi,
I have some questions,
Can I find miRNA in DepMap Public 21Q3? Where can I find it? I’m interested in working in cell lines. I found the data about transcript CCLE_RNAseq_transcripts.csv is 3.2 GB, and the other is CCLE_expression_transcripts_expected_count.csv is 1.4GB. What is the difference between these files?
Thank you

2

Hi, you can find the miRNA data on the portal download page. Here’s a link to the data.

As of the other files you can find the documentation on the portal download page when you click on the file. I’m pasting the information here for your reference:

CCLE_RNAseq_transcripts.csv:

RNAseq transcript tpm data using RSEM. Log2 transformed, using a pseudo-count of 1. - Rows: cell lines (Broad IDs) - Columns: transcripts (HGNC symbol and ensembl transcript ID)

CCLE_expression_transcripts_expected_count.csv

RNAseq read count data from RSEM. - Rows: cell lines (Broad IDs) - Columns: transcripts (HGNC symbol and ensembl transcript ID)

3

Thank you so much jnoorback. Blessings :slight_smile: