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Cell Line selection based on RPE for func analysis
Hi, using the Data explorer, and relative protein expression, I checked the genes of interest on X & Y axis and found a couple of cell lines. Since both the genes of interests seem to have...
View ArticleCould I access the CRISPR screen log fold change or raw screening data
Hi, i was wondering if i’m interested in some certain cell lines and would like to have the relatively raw CRISPR KO screen data (eg. log fold change or even read counts), how could I get access to...
View ArticleAchilles common essentials in 23Q2
Hello DepMap Team, I was using both post-Chronos “Achilles_common_essentials” and “CRISPR_common_essentials” from 22Q1 dataset in my project. I am currently updating my results according to 23Q2...
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Do the values in CCLE_RNAseq_reads_v2.csv represent raw count data or...
depmap.org DepMap Data Downloads The latest quarterly release and archive of available datasets 2 posts - 2 participants Read full topic
View ArticleCopy number for Y-chromosome genes
I am hoping to get some clarification on how the copy number values are calculated for Y-chromosome genes. Given that the copy number value is calculated as log2(relative CN + 1), what is the relative...
View ArticleRVH421SKINFV1 cell line
Does anyone know where to buy the DepMap RVH421SKINFV1 cell line from? It’s also known as RVH-421 Dab-R. The parent is RVH-421, but I can’t find the derivative anywhere. Any leads would be greatly...
View ArticleCOSMIC hotspot mutations
Hi everyone, I want someone to explain to me: The difference between the “damaging_effect.csv” and “hotspot.csv” files? What does it mean the column “CosmicHotspot” in the “OmicsSomaticMutations.csv”...
View ArticleHow to save lists.
Is it possible to save you cell line and gene specific lists so that you dont have to recreate them every time you use DepMap? 1 post - 1 participant Read full topic
View ArticleCRISPR (DepMap Public 23Q2+Score, Chronos) - download
Hi, When searching for a gene, we can view the corresponding CRISPR score (DepMap Public 23Q2+Score, Chronos): 1094/1095. Is there a downloadable file for all genes containing this value (e.g....
View ArticleExpression pattern for transcripts from 23Q2 vs 22Q4 data
Dear All, I wanted to analyze the expression of different isoforms of a specific gene in particular cell lines, and I discovered that the expression patterns are completely different for the 23Q2 and...
View ArticleWhy is the Chronos dependency score smaller than -1?
Hi, I am trying to identify genes that are essential for my target cells. According to the introduction, if the score is close to -1, it means that the gene is essential for the cells. However, I have...
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Using of the images generated by DepMap for publications
Should I get permission for publication of the images generated by DepMap, for example this one: ? 1 post - 1 participant Read full topic
View ArticleDNMT3A R635W Mutation in OCIAML2 annotation inconsistency
Hi, I noticed annotation inconsistency of the DNMT3A R635W mutation in OCIAML2. If I search for OCIAML2 cell line in the DepMap portal, DNMT3A R635W is annotated as “likely oncogenic” and “likely...
View ArticleUsing DepMap transcriptomic data to select a cell line where a gene is not...
Hi! I am working to select a cell line for a functional study, and am looking for a cell line that doesn’t express the target gene, so we can test the effect of mutant genes. Is there a common process...
View ArticleDiscovering Compensatory Mechanisms
I am new to this tool and am trying to identify compensatory mechanisms for my gene of interest. When ever I try to look at expression, it only shows different cell lines. How can I look at...
View ArticleProtein Array names issue
Hi DepMap team, We encountered some relatively minor issues related to the Protein Array (RPPA) data which may be of interest to you. Several protein names in the downloaded Protein_Array.csv file are...
View ArticleAch-002335_u-ch1
Hi, I can’t find the above cell line in DepMAP, but found the accession number in Cellosaurus. Has the data been deleted, and if so, is there a problem with this cell line? Thanks! 2 posts - 2...
View ArticleSaved PNG is without data points
Hi there, I was just trying to save the 2D Landscape and Biomarker plots (DepMap - Broad Institute). The downloaded png file does not show any data points. It would be great getting according plots...
View ArticleWhat are those ERCC genes in RNASeq data of 21Q1?
Hi, there: for some reasons, I have to analyze the old RNAseq data from 21Q1 and I used DESeq2 package. In one of contrasts, there are lots of ERCC alike genes showed up in my differential gene list....
View ArticleCell Line Molecular Subtypes
Hi, I’m looking for a file that has all cell lines listed along with their molecular subtypes. I know in 23Q2, Model.csv has some listed under LegacyMolecularSubtype, but I’m wondering if there’s...
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