# \#genetic-screens **URL:** https://forum.depmap.org/tag/genetic-screens/3.md [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) --- ## [Reconstructing WRN broken-(TA)n FPBM with 26Q3 public WGS: systematic ~8.6% scale shift](https://forum.depmap.org/t/reconstructing-wrn-broken-ta-n-fpbm-with-26q3-public-wgs-systematic-8-6-scale-shift/4700)
**Author:** [@f-drakeland](https://forum.depmap.org/u/f-drakeland)\ **Replies:** 0\ **Last updated:** [October 21, 2026, 4:46pm UTC](https://forum.depmap.org/t/reconstructing-wrn-broken-ta-n-fpbm-with-26q3-public-wgs-systematic-8-6-scale-shift/4700 "2026-10-21T16:46:44Z")
Hi all, I’ve been working on a reproducibility project using current DepMap/CCLE public WGS data and wanted to ask about a pattern I found in the reconstruction. I reconstructed the broken-(TA)n repeat phenotype (FPBM)… --- ## [CNV correction](https://forum.depmap.org/t/cnv-correction/4607)
**Author:** [@bav](https://forum.depmap.org/u/bav)\ **Replies:** 0\ **Last updated:** [April 8, 2026, 8:19pm UTC](https://forum.depmap.org/t/cnv-correction/4607 "2026-04-08T20:19:20Z")
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, WNT2, CTTNBP2, KCND2) a… --- ## [Culture medium question about pyruvate](https://forum.depmap.org/t/culture-medium-question-about-pyruvate/4600)
**Author:** [@Bimo](https://forum.depmap.org/u/Bimo)\ **Replies:** 3\ **Last updated:** [March 31, 2026, 2:36am UTC](https://forum.depmap.org/t/culture-medium-question-about-pyruvate/4600 "2026-03-31T02:36:12Z")
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 basic DMEM. Our lab pr… --- ## [is CRIPSRGeneEffect X and Y chromosome aware](https://forum.depmap.org/t/is-cripsrgeneeffect-x-and-y-chromosome-aware/4575)
**Author:** [@bommisetti11](https://forum.depmap.org/u/bommisetti11)\ **Replies:** 1\ **Last updated:** [February 12, 2026, 3:02pm UTC](https://forum.depmap.org/t/is-cripsrgeneeffect-x-and-y-chromosome-aware/4575 "2026-02-12T15:02:09Z")
Hello, I am pretty new to using this database, but I was recently trying to analyze CRISPRGeneeffect of certain paralog proteins that are present either on X or Y chromosomes. XX individuals would have two copies of X v… --- ## [Has Chronos2 been adopted in DepMap 25Q3 for gene-effect estimation?](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539)
**Author:** [@Jeffrey25](https://forum.depmap.org/u/Jeffrey25)\ **Replies:** 1\ **Last updated:** [January 6, 2026, 8:59pm UTC](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539 "2026-01-06T20:59:53Z")
Hi DepMap team, I have a question regarding the model used for gene-effect estimation in the most recent releases. I’m aware that Chronos was introduced starting in DepMap 21Q3. Recently, a new version — Chronos2 — wa… --- ## [mutation query](https://forum.depmap.org/t/mutation-query/4473)
**Author:** [@ciaraduit](https://forum.depmap.org/u/ciaraduit)\ **Replies:** 1\ **Last updated:** [September 23, 2025, 6:30pm UTC](https://forum.depmap.org/t/mutation-query/4473 "2025-09-23T18:30:47Z")
Hi! I was looking at the mutations section under Characterisation of the CACNA1D gene, and did not find that my cell line of interest had a mutated CACNA1D. However in the COSMIC database I did. Is there any way of kno… --- ## [Drug-Target validation using CRISPR and PRISM repurposing dataset](https://forum.depmap.org/t/drug-target-validation-using-crispr-and-prism-repurposing-dataset/4268)
**Author:** [@Mohamed\_El\_Moussaoui](https://forum.depmap.org/u/Mohamed_El_Moussaoui)\ **Replies:** 6\ **Last updated:** [July 1, 2025, 9:01am UTC](https://forum.depmap.org/t/drug-target-validation-using-crispr-and-prism-repurposing-dataset/4268 "2025-07-01T09:01:01Z")
Hello, i am working on validating Drug-target screens to validate the hypothesis that the drug is inhibiting the gene product by examining that the gene ko and the drug have similar signatures (effects). however, i am lo… --- ## [Regarding CRISPR data for H69](https://forum.depmap.org/t/regarding-crispr-data-for-h69/4280)
**Author:** [@debojit\_123](https://forum.depmap.org/u/debojit_123)\ **Replies:** 0\ **Last updated:** [June 12, 2025, 8:46pm UTC](https://forum.depmap.org/t/regarding-crispr-data-for-h69/4280 "2025-06-12T20:46:24Z")
Hello, I am seeing an issue regarding the CRISPR data for small cell line neuroendocine data sets. Previously, i found CRISPR score for NCI-H69, now with the new 24Q4+ i am unable to get any CRISPR data for these cell l… --- ## [Cell Line Selection for CRISPR Screen](https://forum.depmap.org/t/cell-line-selection-for-crispr-screen/4087)
**Author:** [@srikarkrishnag](https://forum.depmap.org/u/srikarkrishnag)\ **Replies:** 0\ **Last updated:** [March 23, 2025, 1:17am UTC](https://forum.depmap.org/t/cell-line-selection-for-crispr-screen/4087 "2025-03-23T01:17:52Z")
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 wondering if there is… --- ## [Co-dependency lists?](https://forum.depmap.org/t/co-dependency-lists/4065)
**Author:** [@vasilisgr](https://forum.depmap.org/u/vasilisgr)\ **Replies:** 2\ **Last updated:** [March 14, 2025, 8:08pm UTC](https://forum.depmap.org/t/co-dependency-lists/4065 "2025-03-14T20:08:01Z")
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? --- ## [Details of CRISPR experiment: ScreenSequenceMap.csv](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 4:15pm UTC](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021 "2025-03-07T16:15:08Z")
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 methods but still c… --- ## [Mocs3 interacting drugs](https://forum.depmap.org/t/mocs3-interacting-drugs/4012)
**Author:** [@MikeSusaeta](https://forum.depmap.org/u/MikeSusaeta)\ **Replies:** 0\ **Last updated:** [February 26, 2025, 9:14am UTC](https://forum.depmap.org/t/mocs3-interacting-drugs/4012 "2025-02-26T09:14:08Z")
Hello, I am a 3rd year PhD student looking to understand how can I look for the CRISPR libraries and select an existing compound that could inhibit my gene of interest MOCS3. If you could help me out with this, I would v… --- ## [Clarification on Y-axis height within the same tumor type in expression plot](https://forum.depmap.org/t/clarification-on-y-axis-height-within-the-same-tumor-type-in-expression-plot/3666)
**Author:** [@Giacomo\_Graziano](https://forum.depmap.org/u/Giacomo_Graziano)\ **Replies:** 1\ **Last updated:** [October 18, 2024, 8:55pm UTC](https://forum.depmap.org/t/clarification-on-y-axis-height-within-the-same-tumor-type-in-expression-plot/3666 "2024-10-18T20:55:52Z")
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 heights along the Y-ax… --- ## [CRISPR screen and RNA-seq](https://forum.depmap.org/t/crispr-screen-and-rna-seq/3660)
**Author:** [@matlat](https://forum.depmap.org/u/matlat)\ **Replies:** 2\ **Last updated:** [October 11, 2024, 8:40am UTC](https://forum.depmap.org/t/crispr-screen-and-rna-seq/3660 "2024-10-11T08:40:38Z")
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 and RNA-seq technol… --- ## [Cell lines removed from newer releases](https://forum.depmap.org/t/cell-lines-removed-from-newer-releases/3627)
**Author:** [@danibrotto](https://forum.depmap.org/u/danibrotto)\ **Replies:** 4\ **Last updated:** [October 7, 2024, 2:13pm UTC](https://forum.depmap.org/t/cell-lines-removed-from-newer-releases/3627 "2024-10-07T14:13:38Z")
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 unavailable in the most … --- ## [HSC39 cells](https://forum.depmap.org/t/hsc39-cells/3637)
**Author:** [@NMADHUSU89](https://forum.depmap.org/u/NMADHUSU89)\ **Replies:** 0\ **Last updated:** [October 6, 2024, 11:07pm UTC](https://forum.depmap.org/t/hsc39-cells/3637 "2024-10-06T23:07:17Z")
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 --- ## [Which one of the expression data is proper for machine learning?](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367)
**Author:** [@SongSong](https://forum.depmap.org/u/SongSong)\ **Replies:** 4\ **Last updated:** [September 4, 2024, 2:10am UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367 "2024-09-04T02:10:14Z")
Hi, thank you for your effort in launching the newest dataset version 2024Q2. But I’m a little confused about the two kinds of gene expression data: original and batch normalized. If I want to use the gene expression d… --- ## [How should I interpret changes in top co-dependencies across different datasets?](https://forum.depmap.org/t/how-should-i-interpret-changes-in-top-co-dependencies-across-different-datasets/3337)
**Author:** [@android415](https://forum.depmap.org/u/android415)\ **Replies:** 0\ **Last updated:** [June 12, 2024, 1:06pm UTC](https://forum.depmap.org/t/how-should-i-interpret-changes-in-top-co-dependencies-across-different-datasets/3337 "2024-06-12T13:06:31Z")
Hello everyone, TL;DR: I see different top co-dependencies between the 20Q2 and 24Q2 for the gene CHEK1. I think this might be because the 20Q2 version was calculated using CERES whereas 24Q2 is calculated using Chronos… --- ## [Cell line susceptibility to lentiviral infection](https://forum.depmap.org/t/cell-line-susceptibility-to-lentiviral-infection/3150)
**Author:** [@mte](https://forum.depmap.org/u/mte)\ **Replies:** 3\ **Last updated:** [April 5, 2024, 4:53pm UTC](https://forum.depmap.org/t/cell-line-susceptibility-to-lentiviral-infection/3150 "2024-04-05T16:53:47Z")
Does the DepMap team have metadata on the susceptibility of different cell lines to lentiviral infection? It would be very useful to know how easy it is to infect different DepMap cell lines with lentiviral libraries, as… --- ## [Selective dependencies](https://forum.depmap.org/t/selective-dependencies/3133)
**Author:** [@anandselvaraj](https://forum.depmap.org/u/anandselvaraj)\ **Replies:** 1\ **Last updated:** [April 5, 2024, 1:18pm UTC](https://forum.depmap.org/t/selective-dependencies/3133 "2024-04-05T13:18:48Z")
Is there a downloadable list of all selectively dependent genes called by both CRISPR and RNAi ? --- ## [Viability test used?](https://forum.depmap.org/t/viability-test-used/3174)
**Author:** [@Giacomo\_Graziano](https://forum.depmap.org/u/Giacomo_Graziano)\ **Replies:** 0\ **Last updated:** [April 2, 2024, 5:56pm UTC](https://forum.depmap.org/t/viability-test-used/3174 "2024-04-02T17:56:11Z")
If I knocked down the “A” gene using technologies such as RNAi, in two cell lines with opposite dependencies for that gene, how can I evaluate the different dependency? Would a difference in cell growth be observable aft… --- ## [Definition of common essential genes](https://forum.depmap.org/t/definition-of-common-essential-genes/3171)
**Author:** [@Allan\_Lui](https://forum.depmap.org/u/Allan_Lui)\ **Replies:** 0\ **Last updated:** [April 2, 2024, 1:00am UTC](https://forum.depmap.org/t/definition-of-common-essential-genes/3171 "2024-04-02T01:00:51Z")
In the web portal, common essential genes are defined as: A gene which, in a large, pan-cancer screen, ranks in the top X most depleting genes in at least 90% of cell lines. X is chosen empirically using the minimum of t… --- ## [Categorization of Cell Lines by DepMap Release Date](https://forum.depmap.org/t/categorization-of-cell-lines-by-depmap-release-date/3075)
**Author:** [@bleslie](https://forum.depmap.org/u/bleslie)\ **Replies:** 2\ **Last updated:** [March 7, 2024, 4:02pm UTC](https://forum.depmap.org/t/categorization-of-cell-lines-by-depmap-release-date/3075 "2024-03-07T16:02:15Z")
Hi all, I’m trying to track the order of the addition of new cell lines to DepMap. I’d like to know what was the first release that included CRISPR screen data for a particular cell line, for the entire dataset. I do no… --- ## [RNA-seq paired with CRISPR screen data?](https://forum.depmap.org/t/rna-seq-paired-with-crispr-screen-data/3107)
**Author:** [@wshao](https://forum.depmap.org/u/wshao)\ **Replies:** 1\ **Last updated:** [March 5, 2024, 5:26pm UTC](https://forum.depmap.org/t/rna-seq-paired-with-crispr-screen-data/3107 "2024-03-05T17:26:55Z")
Is the RNA-seq data from “OmicsExpressionProteinCodingGenesTPMLogp1.csv” paired with the CRISPR essentiality data from “CRISPRGeneDependency.csv” and “CRISPRGeneEffect.csv”? i.e. was the same group of cells split in two … --- ## [How to interpret the results about "effect size"](https://forum.depmap.org/t/how-to-interpret-the-results-about-effect-size/423)
**Author:** [@cornelius](https://forum.depmap.org/u/cornelius)\ **Replies:** 6\ **Last updated:** [December 12, 2023, 6:55pm UTC](https://forum.depmap.org/t/how-to-interpret-the-results-about-effect-size/423 "2023-12-12T18:55:25Z")
I tried to find the dependency in a specific genetic background. So, I selected two groups of cancer cell lines ,a control group and a genetic variant group, to find the dependent genes in the genetic variant group using… --- ## [Where is probability of dependency used?](https://forum.depmap.org/t/where-is-probability-of-dependency-used/49)
**Author:** [@Jose](https://forum.depmap.org/u/Jose)\ **Replies:** 3\ **Last updated:** [October 24, 2023, 4:23pm UTC](https://forum.depmap.org/t/where-is-probability-of-dependency-used/49 "2023-10-24T16:23:18Z")
When looking at the overview page of a gene it mentions that a cell line is considered dependent if it has a probability of dependency of greater than 0.5., but when I click view details there is no mention of a dependen… --- ## [Could I access the CRISPR screen log fold change or raw screening data](https://forum.depmap.org/t/could-i-access-the-crispr-screen-log-fold-change-or-raw-screening-data/2872)
**Author:** [@Yanjing\_Liu](https://forum.depmap.org/u/Yanjing_Liu)\ **Replies:** 1\ **Last updated:** [October 24, 2023, 3:27am UTC](https://forum.depmap.org/t/could-i-access-the-crispr-screen-log-fold-change-or-raw-screening-data/2872 "2023-10-24T03:27:31Z")
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 them? Many thanks! --- ## [Some genes have 2 labels; common essential and strongly selective](https://forum.depmap.org/t/some-genes-have-2-labels-common-essential-and-strongly-selective/2825)
**Author:** [@anandselvaraj](https://forum.depmap.org/u/anandselvaraj)\ **Replies:** 1\ **Last updated:** [September 22, 2023, 8:55pm UTC](https://forum.depmap.org/t/some-genes-have-2-labels-common-essential-and-strongly-selective/2825 "2023-09-22T20:55:25Z")
Some genes like TRIM37 and CDK11 are labeled as both ‘common essential’ and ‘strongly selective’. Is this an error or a specific double label indicating some special categories? How was this determined? Thanks --- ## [number of investigated cell lines in CRISPR screens. ](https://forum.depmap.org/t/number-of-investigated-cell-lines-in-crispr-screens/2763)
**Author:** [@Luka](https://forum.depmap.org/u/Luka)\ **Replies:** 1\ **Last updated:** [August 16, 2023, 6:45pm UTC](https://forum.depmap.org/t/number-of-investigated-cell-lines-in-crispr-screens/2763 "2023-08-16T18:45:29Z")
Hi, a question regarding CRISPR screens: it seems to me that some genes were KO’d in 1095 cell lines, while others “only” in 317 (presumably in the Score study). Is there a reason why these genes have not been investig… --- ## [Missing CRISPRGeneEffect values in 23Q2 release](https://forum.depmap.org/t/missing-crisprgeneeffect-values-in-23q2-release/2604)
**Author:** [@BastiaanSpanjaard](https://forum.depmap.org/u/BastiaanSpanjaard)\ **Replies:** 1\ **Last updated:** [June 5, 2023, 3:27pm UTC](https://forum.depmap.org/t/missing-crisprgeneeffect-values-in-23q2-release/2604 "2023-06-05T15:27:07Z")
Hi, There seem to be some missing values in the CRISPRGeneEffect.csv-file in the 23Q2 release, a total of 184,785 by my counting. In contrast, that same file in the 22Q4 release had no missing values. The missing values… [Next page](https://forum.depmap.org/tag/genetic-screens/3.md?match_all_tags=true&page=1&tags%5B%5D=genetic-screens)