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Unable to open anything

Trying to choose cell lines based on their GNA13 expression in the pancreas. Unable to open compare expression distribution page and anything else relating to expression. Error received when trying to...

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Drug screen data is not availbale or is it chnaged the way we used to access it

Dear DepMap members, I am interested in checking the drug sensitivity of melanoma lines to atorvastatin drug and other drugs in relation to the LDLR protein levels. In the past I used to see the...

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Details of CRISPR experiment: ScreenSequenceMap.csv

Hello, I would like to know the specific process of conducting CRISPR experiments on DepMap However, I couldn’t find the ScreenSequenceMap.csv mentioned on the webpage. I also tried other search...

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Prism secondary drug screening unable to download (google cloud access denied)

Hi DepMap team, Looks like we are all unable to download the PRISM secondary drug screening results. My error message is “google cloud access denied”. Could you please help solve this issue? Thank you...

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Metadata for ssGSEA pathways

Hello all, I am having trouble finding information about the gene set enrichment pathways (columns) in ssGSEA_Public_24Q2_subsetted. For example, I would like to know which genes are included in each...

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Annotation version for each release

Hi everyone, I have been looking through different GitHub pages and different parts of the website, but I couldn’t locate a page for the annotation used for each release. Is there a page where the...

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WGS MAF file

Where can I find mutation data for HCC1143 WGS regions? The OmicsSomaticMutations file I downloaded seems to be mostly covering exonic regions and very few intronic regions and I’m actually interested...

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Row names in the OmicsExpressionTranscripts file

Hi, I have a simple question about the OmicsExpressionTranscriptsTPMLogp1Profile file. When I tried to match the row names in it to the model name, I couldn’t find the related information in...

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Co-dependency lists?

Was wondering if there is a place I can download the full CRISPR co-dependencies (not just top 100), meaning the correlations from DepMap Public 24Q4+Score, Chronos, for all genes? 1 post - 1...

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Batch corrected Expression Public 24Q4 - What base?

Hey! I am unsure what base the Batch corrected Expression Public 24Q4 expression data comes in. I used the “Create and download a customized dataset” page and selected/downloaded the Batch corrected...

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list of essential genes for the survival of colorectal cancer cells

I am a data scientist and have recently started working with biological data. I need some guidance: Which version of the dataset should I use to obtain the list of essential genes for the survival of...

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Mesenchymal models

A while ago, I performed a DepMap analysis to find the mean gene effect on Meshenchymal models, as shown in the attached image. Currently, I’m trying to repeat the same query using different...

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Cell Line Selection for CRISPR Screen

Hi, This may be a very naive question - apologies in advance. Any help would be much appreciated. I’m trying to design a CRISPR base-editing screen for a list of oncogenes and tumorsupressors. I’m...

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Availability of RNA-seq data after drug treatment

Hello, I am looking for RNA-seq data of cancer cell lines treated with specific drugs. Could you please provide information on where I can find these datasets within DepMap or if they are available...

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Multiple SMILES in secondary-screen-dose-response-curve-parameters.csv

Hello, I hope this message finds you well. I am currently working with the dataset in the file secondary-screen-dose-response-curve-parameters.csv and noticed that the “smiles” column contains...

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Availability of of RNA-seq bigwig files

Hello, I am looking for RNA-seq genome-wide coverage data in bigwig format (instead of table with expression per gene). Is this level of data available? Or a level of data that could be converted to...

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Normalization -TMM

Hi I want to understand that if I have to do TMM normalization rather than using TPM as TPM is not considered a very good parameter to compare across different samples. Which file with Raw reads would...

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Negative goodness of fit

Dear DepMap team, Why some r2 values in the Prism secondary-screen-dose-response-curve-parameters.csv file are negative? Isn’t r2 bounded between 0 and 1? Thanks 1 post - 1 participant Read full topic

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Non-breaking space in Model.csv current version (2024Q4)

Hi - Minor but I hit a potential problem using the current (2024Q4) version of Model.csv. For the entry for model ID ACH-000938, for the field ModelSubtypeFeatures, it contains “DUX4” and then some...

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error in custom analysis

I’m trying to compare the CRISPR dependencies of one cell line vs two other cell lines. It returns an unexpected error. 2 posts - 2 participants Read full topic

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IC50 unit of measure

Hi, In the file “Drug_sensitivity_AUC_(CTD^2)_subsetted” Are the IC50 values informed in micromolar? If so, what do negative values mean? Was the concentratation range (7.8-2000 nM) the same for all...

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GDSC or CTD2 data in data explorer?

Hi As always great to have DepMap and the Data Explorer tool! Question - in Data Explorer it seems I’m able to drug screen data just for the PRISM screens (which are great) but not GDSC or CTD2. Is...

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Availability of VCF/WGS data for cell line demultiplexing

Hi all, I am working with a single-cell RNA-seq experiment where two cell lines, HT29 (COAD) and KP4 (Pancreas), were multiplexed together before sequencing. The data has been aligned to the GRCh38...

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TACC3 AO-252 Phase 1A

A2A Pharmaceuticals has a TACC3 inhibitor in phase 1 for ovarian, triple negative and endometrial cancers. Based on complete regressions preclinically, for these indications as well as gastric and...

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Batch corrected counts data

Is there a batch-corrected version of the counts data, that combines the stranded and unstranded RNA-seq profiles? I see there is a batch-corrected form of the log(TPM+1) counts, so I assume the...

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Reference genome for mutation data

Hi, we are looking at the list of mutations for DU145 cell line ( DepMap ID: ACH-000979) and guessing the position is from hg38 genome, can you please confirm this? Thank you very much in advance! 2...

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Issue with Drug sensitivity AUC (CTD^2)

Hi, I am encountering an issue while downloading the Drug Sensitivity AUC (CTD^2) file from the custom download section. Specifically, the values in the file do not appear to be AUC scores, as they...

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DepMap portal cell line mutation,

Hello, What version does the DepMap portal use currently to annotate a mutation in a cancer cell line with the default setting? A couple of cell lines showed a different mutation pattern between cBio...

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NCI-H854 Oncotree cancer type

Hi, NCI-H854 was annotated as a lung cancer in 2019, but is now annotated as a colorectal cancer model. Was there a documented reason for this change? It is also annotated as being from a primary...

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Prism compound and cell line count

Hello Community, I´m not sure if this exact question has been asked before. After going through some posts I could not find an answer which is why I´m trying it this way. The main question is: How...

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