Organoid dependency data

Q&A
1

I tried to find the recently published 3D tumor organoid dependency dataset on the DepMap portal without success. Any guidance would be much appreciated!

2

The downloadable files can be found at NextGen Model Manuscript 2026.

If you’re looking for it in data explorer, you can find it using these settings:

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Thanks,

Phil

3

Hi,
Just wondering, are there plans to also release the count level data for these models? From what I see in the “NextGen Model Manuscript 2026 Files” only log2(TPM+1) values are available in the “next_gen_expression.csv” file.
Thanks!

-Dan

4

Important point for downstream analysis. DESeq2 and edgeR require unnormalized integer counts, so requesting raw matrix drops via the DepMap contact form helps prioritize future releases.

5

I also struggle to find the organoid dataset, I tried @pmontgom Density 1D, points CRISPR - however there is no option to add NextGen Model or no CRISPR+NextGen Model. will it be added soon?

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6

Hi akacrispr,

CRISPRGeneEffect scores for organoid models can be found by filtering based on Model Annotation on Data Explorer. Under Primary Annotations, you can identify organoid models by filtering GrowthPattern to be Dome. Another option would be to use the Model.csv file under downloads which has the GrowthPattern information for each ModelID.

Best,

Yejie

7

Just to explain the discrepancy between what’s in the earlier messages and where you can find the data today: When the paper was released, we temporarily created a dataset in Data Explorer called “NextGen Model Manuscript 2026” containing these new screens.

However, since then we’ve released the 26Q3 data, where the organoid lines have been processed with all other CRISPR screens. Since you can now find the new models in the harmonized CRISPR dataset, we’ve removed the temporary dataset. See Yejie’s message for how to find organoid data within CRISPRGeneEffect.csv (which is the name you can find under “Downloads”. This same data is labeled “CRISPR (DepMap Public 26Q3+Score, Chronos)” in Data Explorer)

Thanks,

Phil

8

Now that these models are part of the 26Q3 release, I believe the expression raw counts files should include the new models as well.

Thanks,

Phil