Questions about downloaded data files from depmap

Q&A
1

Hi, there:
I downloaded the following data file from URL: https://depmap.org/portal/download/

CCLE_DepMap_18q3_RNAseq_RPKM_20180718.gct

My questions are:

1.What is the difference between this data file vs the expression data: CCLE_expression_v2.csv at the same URL?

My confusion part is: these RNAseq data is expression data of these cell lines by themselves (cell lines used for DepMap) without any treatment, or these RNAseq data is expression data of these cell lines after depmap treatment such as after RNAi screening in DEMETER or after CRISPR screening for CERES scores?

2.What is difference between Q1, Q2,q3? I know they are different released data for each quarter, but we noticed that one of the cell lines we are interested are only in CCLE_DepMap_18q3_RNAseq_RPKM_20180718.gct, BUT NOT in other Q1, Q2 data files e.g., CCLE_DepMap_18Q1_RNAseq_RPKM_20180214.gct
CCLE_DepMap_18Q2_RNAseq_RPKM_20180502.gct

Thx so much for your help in advance!
Best

Ming

2
  1. CCLE_expression_v2 is a more recent version of the expression data than the CCLE_DepMap_18q3_RNAseq_RPKM_20180718 you downloaded, and will therefore include more cell lines and more up-to-date methods. The CCLE_expression_v2 comes from the 20Q2 (2020, quarter 2) data release, while CCLE_DepMap_18q3_RNAseq_RPKM_20180718 comes from 18Q3 (2018, quarter 3) release. These data also differ in their normalizations - CCLE_expression_v2 is TPM normalized, while CCLE_DepMap_18q3_RNAseq_RPKM_20180718 uses RPKM. Data shown under the top downloads points to the most recent data for a selection of datasets.
    The RNAseq data we provide is expression of the cell lines themselves, without any treatment or genetic perturbation.
  2. Q1, Q2, q3 refer to the quarterly data releases, with Q1 (quarter 1) referring to the first quarter of the year, and Q4 referring to the last quarterly data release of the year. The value (in this case 18) coming before the quarterly number refers to the year of the data release (in this case 2018). 18q3 contains cell lines not found in 18Q1 and 18Q2 as it is a more recent data release. As of today (September 8th, 2020) the most recent released data is 20Q2.
1 Like
3

Really appreciated your input! Ming