# Q&A **URL:** https://forum.depmap.org/c/qa/5.md?page=4 [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) **Page:** 5 --- ## ["Request for Academic Lab Source Information](https://forum.depmap.org/t/request-for-academic-lab-source-information/3937)
**Author:** [@yasaman.barekatain](https://forum.depmap.org/u/yasaman.barekatain)\ **Replies:** 0\ **Last updated:** [January 31, 2025, 1:56pm UTC](https://forum.depmap.org/t/request-for-academic-lab-source-information/3937 "2025-01-31T13:56:33Z")
Hi, for the cell lines listed with “academic lab” as the source, could we get more information about which specific lab they came from? Thank you! --- ## [Clarification on Negative Values in Log-Transformed Gene Expression Data](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902)
**Author:** [@madhu](https://forum.depmap.org/u/madhu)\ **Replies:** 1\ **Last updated:** [January 30, 2025, 10:08pm UTC](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902 "2025-01-30T22:08:23Z")
I am working with the DepMap expression datasets, and I have a question regarding the log-transformed values in the OmicsExpressionProteinCodingGenesTPMLogp1.csv file. As per the dataset documentation, the expression va… --- ## [Omic signatures discrepancies](https://forum.depmap.org/t/omic-signatures-discrepancies/3931)
**Author:** [@AArora](https://forum.depmap.org/u/AArora)\ **Replies:** 1\ **Last updated:** [January 30, 2025, 3:41pm UTC](https://forum.depmap.org/t/omic-signatures-discrepancies/3931 "2025-01-30T15:41:36Z")
Hi DepMap team, I am looking at features like Aneuploidy, WGD etc in the OmicsSignatures.csv files - between 24Q2 and 24Q4 version. There are some cell lines that show discordant values and some that were available befo… --- ## [GDSC1 and GDSC2 AUC data](https://forum.depmap.org/t/gdsc1-and-gdsc2-auc-data/3912)
**Author:** [@Wollvey](https://forum.depmap.org/u/Wollvey)\ **Replies:** 0\ **Last updated:** [January 16, 2025, 3:28pm UTC](https://forum.depmap.org/t/gdsc1-and-gdsc2-auc-data/3912 "2025-01-16T15:28:17Z")
Hello, Is there a method to find the original AUC data from these datasets? Rather being in terms of 0-1, I’m looking for a resource that can provide these AUC numbers in terms of dosage (uM) \* hours. Is this possible? … --- ## [OmicsSomaticMutations.csv, multiple mutation rows of the same cell-line and the same gene](https://forum.depmap.org/t/omicssomaticmutations-csv-multiple-mutation-rows-of-the-same-cell-line-and-the-same-gene/3896)
**Author:** [@mw222](https://forum.depmap.org/u/mw222)\ **Replies:** 2\ **Last updated:** [January 10, 2025, 9:16pm UTC](https://forum.depmap.org/t/omicssomaticmutations-csv-multiple-mutation-rows-of-the-same-cell-line-and-the-same-gene/3896 "2025-01-10T21:16:07Z")
Just want to reiterate how thankful I am for all the helpful and quick responses I have had about this dataset. I had a question regarding the OmicsSomaticMutations dataset that is in MAF format. I am a bit naive when i… --- ## [CRISPR Dual-Knockout screening](https://forum.depmap.org/t/crispr-dual-knockout-screening/3891)
**Author:** [@SongSong](https://forum.depmap.org/u/SongSong)\ **Replies:** 0\ **Last updated:** [January 8, 2025, 6:33am UTC](https://forum.depmap.org/t/crispr-dual-knockout-screening/3891 "2025-01-08T06:33:20Z")
Hi, I have a simple question about the CRISPR Dual-Knockout (CDKO) screening in the DepMap portal. In this paper, the authors mentioned that ‘DepMap also consists of drug-gene and gene-gene combinatorial CRISPR screens’… --- ## [Aneuploidy score](https://forum.depmap.org/t/aneuploidy-score/3883)
**Author:** [@SusanaVM](https://forum.depmap.org/u/SusanaVM)\ **Replies:** 1\ **Last updated:** [January 6, 2025, 10:04pm UTC](https://forum.depmap.org/t/aneuploidy-score/3883 "2025-01-06T22:04:03Z")
Hi all, In the previous Depmap platform there use to be the aneuplidy score dataset. I cannot find it any longer. Could you help me, please? --- ## [DemMap's call for cancer models](https://forum.depmap.org/t/demmaps-call-for-cancer-models/3875)
**Author:** [@yussi](https://forum.depmap.org/u/yussi)\ **Replies:** 2\ **Last updated:** [January 6, 2025, 4:50am UTC](https://forum.depmap.org/t/demmaps-call-for-cancer-models/3875 "2025-01-06T04:50:45Z")
Hello everyone, I wanted to clear a confusion regarding depmap’s call for cancer models initiative. As it seems an open call to submit cancer models, i was wondering, if the characterization and screenings on the cancer … --- ## [Non-Cancerous and Primary or Metastatic cell lines](https://forum.depmap.org/t/non-cancerous-and-primary-or-metastatic-cell-lines/3806)
**Author:** [@Saed\_Sayad](https://forum.depmap.org/u/Saed_Sayad)\ **Replies:** 1\ **Last updated:** [January 2, 2025, 8:22pm UTC](https://forum.depmap.org/t/non-cancerous-and-primary-or-metastatic-cell-lines/3806 "2025-01-02T20:22:15Z")
Hi, How come some of Non-Cancerous cases have Primary or Metastatic labels? Best, Saed OncotreePrimary Disease PrimaryOrMetastasis Count Non-Cancerous Metastatic 4 Non-Cancerous Primary 15 Non-Cancerous 1… --- ## [Chronos score](https://forum.depmap.org/t/chronos-score/3819)
**Author:** [@hjt](https://forum.depmap.org/u/hjt)\ **Replies:** 1\ **Last updated:** [January 2, 2025, 2:17pm UTC](https://forum.depmap.org/t/chronos-score/3819 "2025-01-02T14:17:56Z")
I would like to know if a gene effect Chronos score greater than 0 indicates that the growth rate of the cell line will increase after the gene is knocked out. I have noticed that there are many genes with a score greate… --- ## [MicroRNA codes](https://forum.depmap.org/t/microrna-codes/3874)
**Author:** [@ayaqinuddin](https://forum.depmap.org/u/ayaqinuddin)\ **Replies:** 0\ **Last updated:** [December 30, 2024, 5:21pm UTC](https://forum.depmap.org/t/microrna-codes/3874 "2024-12-30T17:21:49Z")
How can i know the microRNA codes in the downloaded data from DepMap stands for which microRNA --- ## [Cell viability data](https://forum.depmap.org/t/cell-viability-data/3791)
**Author:** [@shenzhong](https://forum.depmap.org/u/shenzhong)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 2:32pm UTC](https://forum.depmap.org/t/cell-viability-data/3791 "2024-12-20T14:32:23Z")
Hello, I would like to know how can I retrieve the cell viability data based on RNAi or CRISPR in human lung cancer cell lines? What does ‘Effect Size Means Difference’ mean in the dependencies enriched data if the numb… --- ## [cell line id](https://forum.depmap.org/t/cell-line-id/3818)
**Author:** [@hjt](https://forum.depmap.org/u/hjt)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 2:18pm UTC](https://forum.depmap.org/t/cell-line-id/3818 "2024-12-20T14:18:19Z")
I have a question. I have a cell line number in each row of this table that is not a depmap ID. However, I need to convert these cell lines to depmap IDs in batches, otherwise my work will be difficult to carry out in th… --- ## [Why isn't all of the cell line annotation data in one place?](https://forum.depmap.org/t/why-isnt-all-of-the-cell-line-annotation-data-in-one-place/3828)
**Author:** [@Andrew\_Cherniack](https://forum.depmap.org/u/Andrew_Cherniack)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 2:16pm UTC](https://forum.depmap.org/t/why-isnt-all-of-the-cell-line-annotation-data-in-one-place/3828 "2024-12-20T14:16:28Z")
The model.csv table contains important annotations such as breast cancer ER, PR and HER2 status which does not seem to be in context manager. However the context manager has information such as extensive MSI/MSS calls wh… --- ## [Absolute copy number ](https://forum.depmap.org/t/absolute-copy-number/3834)
**Author:** [@beckyliu](https://forum.depmap.org/u/beckyliu)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 2:13pm UTC](https://forum.depmap.org/t/absolute-copy-number/3834 "2024-12-20T14:13:12Z")
The current data version has been upgraded to 24Q2, and there is also Gene-level absolute copy number data (OmicsAbsoluteCNGene.csv). Why is the copy number data displayed on the interface still from the CCLE 2019 versio… --- ## [What file is suitable for differential expression analysis](https://forum.depmap.org/t/what-file-is-suitable-for-differential-expression-analysis/3768)
**Author:** [@efraim\_shilo\_shine](https://forum.depmap.org/u/efraim_shilo_shine)\ **Replies:** 4\ **Last updated:** [December 9, 2024, 4:07am UTC](https://forum.depmap.org/t/what-file-is-suitable-for-differential-expression-analysis/3768 "2024-12-09T04:07:38Z")
hi, I would like to perform differential expression analysis between cell line. for that I need raw count expression data. I wonder what file is suitable for this matter as I saw several different read count files thank… --- ## [Stable URL for current release files](https://forum.depmap.org/t/stable-url-for-current-release-files/3765)
**Author:** [@Asa\_Sivertsson](https://forum.depmap.org/u/Asa_Sivertsson)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 5:46pm UTC](https://forum.depmap.org/t/stable-url-for-current-release-files/3765 "2024-12-04T17:46:46Z")
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 Portal in the Atlas. … --- ## [Batch\_corrected\_Expression\_Public\_24Q2](https://forum.depmap.org/t/batch-corrected-expression-public-24q2/3767)
**Author:** [@Nilabja\_Bhattacharje](https://forum.depmap.org/u/Nilabja_Bhattacharje)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 5:40pm UTC](https://forum.depmap.org/t/batch-corrected-expression-public-24q2/3767 "2024-12-04T17:40:06Z")
I have downloaded Batch\_corrected\_Expression\_Public\_24Q2 data. I understood that they have integrated Project Achilis and Score’s dataset. But, how ? What is the total preprocessing and data cleaning pipeline ?? I tried … --- ## [24Q4 Data - timeline?](https://forum.depmap.org/t/24q4-data-timeline/3788)
**Author:** [@cdeleeuw](https://forum.depmap.org/u/cdeleeuw)\ **Replies:** 1\ **Last updated:** [November 21, 2024, 3:54pm UTC](https://forum.depmap.org/t/24q4-data-timeline/3788 "2024-11-21T15:54:44Z")
Hi, I was wondering if we are still on track to have the 24Q4 data uploaded in November? Hoping to start some work and would prefer latest datasets if it’ll be available before the end of the month. Thanks, --- ## [sample ID not match in 'OmicsFusionFiltered' and 'OmicsFusionUnfilteredProfile'](https://forum.depmap.org/t/sample-id-not-match-in-omicsfusionfiltered-and-omicsfusionunfilteredprofile/3789)
**Author:** [@porakim](https://forum.depmap.org/u/porakim)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 9:34pm UTC](https://forum.depmap.org/t/sample-id-not-match-in-omicsfusionfiltered-and-omicsfusionunfilteredprofile/3789 "2024-11-20T21:34:19Z")
Hi, Could you provide matched sample ID in these two files? These files use different sample ID. OmicsFusionFiltered shows the ModelID, but OmicsFusionUnfilteredProfile file shows the ProfileID. I would appreciate if … --- ## [WGS data](https://forum.depmap.org/t/wgs-data/3790)
**Author:** [@porakim](https://forum.depmap.org/u/porakim)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 9:31pm UTC](https://forum.depmap.org/t/wgs-data/3790 "2024-11-20T21:31:35Z")
Hi I see the WGS data from ENA Browser. It says there are 329 cell lines’ WGS data. But, from Data | DepMap Portal, I see 559 cell lines’ WGS data. I wonder where and when I can download the rest of the WGS data. Cou… --- ## [What's the genome version and gene annotation file used for Depmap bulk RNA-Seq expression estimation?](https://forum.depmap.org/t/whats-the-genome-version-and-gene-annotation-file-used-for-depmap-bulk-rna-seq-expression-estimation/3792)
**Author:** [@bigbadbo](https://forum.depmap.org/u/bigbadbo)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 9:28pm UTC](https://forum.depmap.org/t/whats-the-genome-version-and-gene-annotation-file-used-for-depmap-bulk-rna-seq-expression-estimation/3792 "2024-11-20T21:28:25Z")
Dear Sir./Madam., Can I know what’s the genome version and gene annotation file (e.g. Gencode or Ensembl, which version) used for Depmap bulk RNA-Seq expression estimation? Thanks, Bo --- ## [IC50 values in PRISM Repurposing 19Q4: Raw or Logarithmic?](https://forum.depmap.org/t/ic50-values-in-prism-repurposing-19q4-raw-or-logarithmic/3766)
**Author:** [@Uji](https://forum.depmap.org/u/Uji)\ **Replies:** 0\ **Last updated:** [November 17, 2024, 2:05am UTC](https://forum.depmap.org/t/ic50-values-in-prism-repurposing-19q4-raw-or-logarithmic/3766 "2024-11-17T02:05:38Z")
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 natural logarithm form… --- ## [Confirming OmicsCNGene.csv "NaN" Interpretations/Assumptions on the X and Y Chromosome](https://forum.depmap.org/t/confirming-omicscngene-csv-nan-interpretations-assumptions-on-the-x-and-y-chromosome/3742)
**Author:** [@mw222](https://forum.depmap.org/u/mw222)\ **Replies:** 1\ **Last updated:** [November 12, 2024, 3:24pm UTC](https://forum.depmap.org/t/confirming-omicscngene-csv-nan-interpretations-assumptions-on-the-x-and-y-chromosome/3742 "2024-11-12T15:24:34Z")
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 individuals or cell… --- ## [Cell line selector - what data does it use for expression?](https://forum.depmap.org/t/cell-line-selector-what-data-does-it-use-for-expression/3740)
**Author:** [@Oliver\_Hickman](https://forum.depmap.org/u/Oliver_Hickman)\ **Replies:** 1\ **Last updated:** [November 8, 2024, 9:59pm UTC](https://forum.depmap.org/t/cell-line-selector-what-data-does-it-use-for-expression/3740 "2024-11-08T21:59:02Z")
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 datset and the results for… --- ## [Problem with Copy Number data](https://forum.depmap.org/t/problem-with-copy-number-data/3724)
**Author:** [@Kamila\_Szumala](https://forum.depmap.org/u/Kamila_Szumala)\ **Replies:** 2\ **Last updated:** [November 7, 2024, 12:19pm UTC](https://forum.depmap.org/t/problem-with-copy-number-data/3724 "2024-11-07T12:19:07Z")
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 found such a file in… --- ## [DepMap Dependency Scores - Recreation](https://forum.depmap.org/t/depmap-dependency-scores-recreation/3710)
**Author:** [@judepops](https://forum.depmap.org/u/judepops)\ **Replies:** 2\ **Last updated:** [November 7, 2024, 9:20am UTC](https://forum.depmap.org/t/depmap-dependency-scores-recreation/3710 "2024-11-07T09:20:06Z")
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 0.5’ However, when us… --- ## [Getting dependent cell line list of strongly selective genes from DepMap (CRISPR + Achilles)](https://forum.depmap.org/t/getting-dependent-cell-line-list-of-strongly-selective-genes-from-depmap-crispr-achilles/1173)
**Author:** [@ujd913](https://forum.depmap.org/u/ujd913)\ **Replies:** 5\ **Last updated:** [February 14, 2022, 10:03pm UTC](https://forum.depmap.org/t/getting-dependent-cell-line-list-of-strongly-selective-genes-from-depmap-crispr-achilles/1173 "2022-02-14T22:03:50Z")
Hi, I want to get the strongly selective genes and cell line names of these genes from all genes and cell lines of DepMap. So, I downloaded a gene dependency summary file from this link and then got the strongly selecti… --- ## [Copy\_Number\_(Absolute) and OmicsAbsoluteCNGene are Different](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 6:09pm UTC](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677 "2024-10-24T18:09:02Z")
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 in terms of the numb… --- ## [Where do i find the the drug tractability data?](https://forum.depmap.org/t/where-do-i-find-the-the-drug-tractability-data/3689)
**Author:** [@David\_Adams](https://forum.depmap.org/u/David_Adams)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 5:48pm UTC](https://forum.depmap.org/t/where-do-i-find-the-the-drug-tractability-data/3689 "2024-10-24T17:48:02Z")
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. [Previous page](https://forum.depmap.org/c/qa/5.md?page=3) [Next page](https://forum.depmap.org/c/qa/5.md?page=5)