Multiple omics expression profiles
Why do some cell lines have multiple SequencingID profiles in OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv? I see that one profile is marked as “IsDefaultEntryForModel”, but I don’t understand...
View ArticleRead ids between SRA fastq and AWS open data bam
Hello, I’ve got a list of read ids corresponding to a CCLE line RNA-seq fastq file uploaded to SRA. I would like to extract the alignments for these reads from available files that I’ve found on AWS...
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Oncogenic relevant fusions in cell lines
Dear DepMap team, We have been working with the fusion dataset (25Q3) and are interested in your thoughts about relevant oncogenic fusions for cancer cell lines. For example, several cell lines have...
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NF2 damaging mutations
Hi, I have been looking into pleural mesothelioma and screening for synthetically lethal targets in NF2-mutant cases. Only two cells lines have been identified as NF2-mutant PM, however a third cell...
View ArticleCulture medium question about pyruvate
Dear DepMap Portal, I was wondering that if the culture medium is with pyruvate or not, especially the cell line with DMEM. There are mutiple DMEM-high glucose choic from thermo fisher is based on...
View ArticleAneuploidy score version in DepMap
Hi, A year ago Ive done an analysis using the aneuploidy score in the data explorer. Now I wanted to recreate this analysis however the data wasnt there anymore. When looking I found a different...
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Announcing the 26Q1 Release
26Q1 DepMap Release Notes MODEL ANNOTATIONS DepMap Subtype Tree The DepMap Subtype Tree has been updated in accordance with the October 9, 2025 OncoTree update, including a large resubtyping for the...
View ArticleCNV correction
Hey Phil, DepMap - I wanted to alert you, that the “copy number effect” seems not to have been corrected for the cell line EBC1, here: DepMap Cell Line Summary. All of its top dependencies (ASZ1,...
View ArticleMissing WGS data for HeLa (ACH-001086) in DepMap / Terra workspace
Hi, I am trying to locate the whole-genome sequencing (WGS) data for the HeLa cell line (ACH-001086). However, I was unable to find any corresponding WGS data in: the DepMap Terra workspace...
View ArticleCTRP AUC values interpretation
Hello everyone, This question was already asked here by someone but I wasn’t satisfied with the answer unfortunately… I have downloaded the CTRPv2.0_2015_ctd2_ExpandedDataset file, I want to use the...
View ArticleCelligner median distances
Hello! I was wondering how the median distance value is calculated in the Celligner “Rank models for selected tumors” page. For example, if I select “Breast” lineage and “All” subtype, is the median...
View ArticleDuplicate entries
I noticed that there are two entries for ACH-003186 in the OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv file, each with different SequencingID and IsDefaultEntryForModel values. Could you...
View ArticleStatistical test used in Custom Analysis (2-class comparison)
I’ve used DepMap’s Custom Analysis 2-class comparison feature to compare three data types between two groups of cell lines : CRISPR Chronos scores Gene expression Metabolite abundance I have two...
View ArticleAneuploidy score version in DepMap
Hi, A year ago Ive done an analysis using the aneuploidy score in the data explorer. Now I wanted to recreate this analysis however the data wasnt there anymore. When looking I found a different...
View ArticleHelp with understanding DepMap Cell line summary
When I type in a cell line, on the right there is a column Header that says “Molecular Subtypes”. Under this it will often say “Level 0”, and under that it might say “CDKN2A-Lof”. What does Level 0...
View ArticleRegarding gene expression and gene effect score
Regarding gene expression and gene effect score, I have found that the mRNA expression of some genes may be unrelated to or inversely proportional to the gene effect score. That is, the greater the...
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Keep getting this error when downloading Cell Line data through custom downloads
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View ArticleRNA pipeline reference availability
I am trying to run the DepMap Omics RNA pipeline on my own data. The pipeline is available here but the genome reference files in the ‘ccleparams’ bucket are not accessible; specifically I’m getting a...
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Error when downloading files using custom download
Hi, I am getting the following error when trying to download drug sensitivity and crispr data using custom download for particular model. Please help me resolving this issue. 1 post - 1 participant...
View ArticleBulk download gene effect z-scores
To whom it may concern, I want to download the gene effect z-scores for all genes in all cell lines. depmap.org DepMap — Verification depmap.org DepMap — Verification … Is there a bulk download option...
View ArticleProvide an open endpoint for latest version retrieval
With the latest changes to the DepMap portal, to add a captcha layer, it is now no-longer possible to programmatically download files. The bulk download option mentioned in the captcha also redirects...
View ArticleHow should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap...
How should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap Public 26Q1? I am working with the DepMap Public 26Q1 files and need to map CRISPRInferredModelEfficacy.csv reproducibly to...
View Article26Q1 OmicsCNGeneWGS.csv normalization
In the 26Q1 OmicsCNGeneWGS.csv release, what is the reported linear copy number ratio normalized against? Does a ratio of ~1.0 incorporate that specific cell line’s own ploidy (e.g. a value of ~1.0...
View ArticleTSS_RRBS_Methylation_Data
I have noticed that some genes are not available in any of the methylation datasets (CCLE_RRBS_TSS_1kb_20180614.txt, CCLE_RRBS_TSS_CpG_clusters_20180614.txt), but seem to be available through the...
View ArticleDiscrepancy between OmicsAbsoluteCNGene and OmicsAbsoluteCNSegmentsProfile
Hi, I was looking at OmicsAbsoluteCNGene values (24Q4) for the gene DCC on chromosome 18q, in relation to the segment value in OmicsAbsoluteCNSegmentsProfile (also 24Q4). For cell line ACH‑000679...
View ArticleAbsolute copy number data release
Was OmicsAbsoluteCNGene.csv discontinued after 24Q4? If so, what’s the recommended replacement for absolute copy number data? Thank you! 2 posts - 2 participants Read full topic
View ArticleOrganoid dependency data
I tried to find the recently published 3D tumor organoid dependency dataset on the DepMap portal without success. Any guidance would be much appreciated! 1 post - 1 participant Read full topic
View ArticleValue-free PTEN model projection for DepMap Public 26Q1?
We are assessing whether a public-model study of untreated baseline total PTEN protein is feasible without opening assay matrices. We are not asking for files yet and do not want assay values or...
View ArticleMissing data on SOD2 gene expression in 26Q1 and 25Q3
In the expression data (both when accessed through the Custom Downloads feature, and when downloading the complete data file) of at least 26Q1 and 25Q3 Public releases there is no data on expression...
View ArticleCells mistakenly assigned as SCLC
I observed that 3 cells are assigned as SCLC but they are other model type, and one cell has a contamination problem ACH-000727, NCI-H2066 is a Lung squamous cell carcinoma (RRID:CVCL_1520)...
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