ERCC spike-ins in RNAseq data
I’m trying to identify differentially expressed genes between two conditions, and would like to use the ERCC spike-ins as control genes when estimating size factors using DESeq2. I can’t find the...
View ArticleCell lines removed from newer releases
Hi! I’m looking to visualize and download CRISPR dependency data from older DepMap releases. I remember that previous versions included more than one chordoma tumor cell line, but they seem to be...
View ArticleHSC39 cells
Has anyone any experience with lentiviral transduction of HSC39 cells? If so would you be willing to share the protocol? This cell line is included in the DepMap 1 post - 1 participant Read full topic
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Error in downloading"CRISPRGeneDependency.csv"24Q2
Oct 2024-Hi, I want to download the data"CRISPRGeneDependency.csv 24Q2" set from Depmap portal (link below) depmap.org Data | DepMap Portal Data Page but It said"you have no permissions" now I cannot...
View ArticleComparing cell lines IC50 (trastuzumab)
Hi I am trying to compare all the breast cancer cell lines IC50 in response to Trastuzumab and to deruxtecan. The search works for cisplatin, but not for those drugs. The drugs are present in the...
View ArticleCRISPRGeneEffect chromosome arm correction (AC-Chronos)
Hi everyone! In this manuscript (A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data | Genome Biology | Full Text) the authors...
View ArticleGene copy number search for CRISPR engineering
I am planning to use CRISPR knock-in to add GFP to the C-terminus of the SPDEF gene in the T-47D cell line. Before proceeding, I want to check the gene copy number of SPDEF to assess the likelihood of...
View ArticleCRISPR screen and RNA-seq
Hi, Do CRISPR screens have whole-transcriptome RNA-seq data (bulk or single-cell) associated to them? How can I extract high level study information containing cell line, type of genetic manipulation...
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Clarification on Y-axis height within the same tumor type in expression plot
Hello, I was analyzing a plot showing the expression of a gene (PHGR1) in LUAD and COAD cell lines, and I noticed that within each tumor type, the points (representing the cell lines) have varying...
View ArticleChemical structures for compounds in PRISM screen
I am trying to obtain chemical structures, in either InChi or SMILES format, for the compounds in the PRISM 24Q2 screen. I’ve checked the file Repurposing_Public_24Q2_Treatment_Meta_Data.csv, but this...
View ArticleCopy_Number_(Absolute) and OmicsAbsoluteCNGene are Different
Hello, I have noticed that there is a significant difference between the Copy_Number_(Absolute) data in the Custom Downloads interface and the OmicsAbsoluteCNGene data in the All Data interface, both...
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SVs, noncoding mutations for CCLE data
Any plans for additional WGS data? Q&A We have released several WGS in 21Q1 and moving forward there will be more WGS instead of WES. At the moment we haven’t had the bandwidth to provide...
View Articlewhere do i find the the drug tractability data?
For example the info on the bottom left of the page: EGFR DepMap Gene Summary ligand, small molecule etc. I am after this info for all genes/proteins in the genome. 1 post - 1 participant Read full...
View ArticleDepMap Dependency Scores - Recreation
Hi, I am trying to recreate the DepMap dependency tag using your RNAi and CRISPR data which is described as: ‘a cell line is considered dependent if it has a probability of dependency greater than...
View ArticleGenes that overlap with segmental duplication regions and/or are flagged by...
Hello, I have a question regarding your DepMap Public 24Q2 dataset, specifically about the file OmicsAbsoluteCNGene.csv. You mentioned the following: “Genes that overlap with segmental duplication...
View ArticleProblem with Copy Number data
Hello! I would like to retrieve data from copy number variants for all cell lines. The most important information for me is the absolute copy number of minor and major alleles for a given segment. I...
View ArticleCell line selector - what data does it use for expression?
Apologies if this is a repeat question, the Q&A search function doesn’t work. What dataset(s) is used for “Expression public 24Q2” in the cell line selector? I have downloaded the CCLE2 RNAseq...
View ArticleConfirming OmicsCNGene.csv "NaN" Interpretations/Assumptions on the X and Y...
Hi, I have noticed in many of the updates that the OmicsCNGene.csv NaN are primarily for Y-chromosome genes. My assumptions are that these are a result of a lack of Y-chromosome mapped segments in XX...
View ArticleStable URL for current release files
Hi, Thank you for a very nice and valuable resource! My name is Åsa and I work for the Human Protein Atlas. We would like to use the CRISPR common essential gene list from this file Data | DepMap...
View ArticleIC50 values in PRISM Repurposing 19Q4: Raw or Logarithmic?
Hello! I am interested in the IC50 values in the secondary-screen-dose-response-curve-parameters.csv file from PRISM Repurposing 19Q4. Could you clarify whether these IC50 values are represented in...
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