Datasetpublic

tahoebio/EmeraldBay

Emerald Bay Emerald Bay is a single-cell perturbation dataset of over 1.8M transcriptomic profiles spanning 52 cell lines and 91 drug treatments, including combinations. Generated using Tahoe Therapeutics's MOSAIC high-throughput platform, it comprises a curated set of anticancer agents applied at multiple doses across a MOSAIC tumor pool optimized for five-day culture. The dataset provides two readouts: a transcriptional profile at single-cell resolution and a drug-phenotype… See the full description on the dataset page: https://huggingface.co/datasets/tahoebio/EmeraldBay.

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Dataset Card

Emerald Bay

Emerald Bay is a single-cell perturbation dataset of over 1.8M transcriptomic profiles spanning 52 cell lines and 91 drug treatments, including combinations. Generated using Tahoe Therapeutics's MOSAIC high-throughput platform, it comprises a curated set of anticancer agents applied at multiple doses across a MOSAIC tumor pool optimized for five-day culture. The dataset provides two readouts: a transcriptional profile at single-cell resolution and a drug-phenotype measure derived from cell-count proportions at the five-day endpoint.

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Quickstart

python

from datasets import load_dataset
# Load dataset in streaming mode
ds = load_dataset("tahoebio/EmeraldBay", streaming=True, split="train")
# View the first record
next(ds.iter(1))

Setting streaming=True instantiates an IterableDataset and prevents needing to download the full dataset first.

Tutorials

Please refer to our tutorials for examples on using the data, accessing metadata tables and converting to/from the anndata format.

Please see the Data Loading Tutorial for a walkthrough on using the data.

<table> <thead> <tr> <th>Notebook</th> <th>URL</th> <th>Colab</th> </tr> </thead> <tbody> <tr> <td>Loading the dataset from huggingface, accessing metadata, mapping to anndata</td> <td> <a href="https://huggingface.co/datasets/tahoebio/EmeraldBay/blob/main/tutorials/loadingdata.ipynb" target="blank"> Link </a> </td> <td> <a href="https://colab.research.google.com/drive/1nbiNW5iJVtb2wn1iXOdvAJHhMAHqZ5BC?usp=sharing" target="_blank"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab"/> </a> </td> </tr> </tbody> </table>

Dataset Features

We provide multiple tables with the dataset including the main data (raw counts) in the expression_data table as well as various metadata in the gene_metadata,sample_metadata,drug_metadata,cell_line_metadata, and summary_statistics tables.

The main data can be downloaded as follows:

python

expression_data = load_dataset("tahoebio/EmeraldBay", "expression_data", split="train")

Per-cell transcriptomic profiles are provided (1,831,648 cells across 116 shards), with each row corresponding to one cell.

The expression_data table has the following fields:

Field	Type	Description
`genes`	`sequence<int64>`	Gene token IDs for genes with non-zero expression in the cell. Aligned with `expressions`. Map to `gene_symbol`/`ensembl_id` via `gene_metadata`.
`expressions`	`sequence<float64>`	Raw count values, aligned with `genes`.
`drug`	`string`	Name of the treatment. `DMSO_TF` marks vehicle controls.
`drugname_drugconc`	`string`	Compound × concentration string (e.g. `"[('Cetuximab', 0.068596, 'uM')]"`), matching the `condition` key in `summary_statistics`.
`cell_line`	`string`	Cellosaurus ID of the cancer cell line (e.g. `CVCL_1055`).
`sample`	`string`	Unique sample identifier (distinguishes replicate treatments).
`BARCODE_SUB_LIB_ID`	`string`	Combination of barcode and sublibrary identifiers. Unique per cell.

Additional metadata

Gene Metadata

python

gene_metadata = load_dataset("tahoebio/EmeraldBay", "gene_metadata", split="train")

The gene_metadata table maps each gene to its integer token ID used in the expression data. It extends the Tahoe-100M gene vocabulary: the first 62,710 rows preserve the Tahoe-100M token IDs verbatim, and 574 additional genes present in EmeraldBay but not Tahoe-100M are appended at the end of the vocabulary.

Column Name	Description
`gene_symbol`	The HGNC-approved gene symbol corresponding to each gene (e.g., TP53, BRCA1).
`ensembl_id`	The Ensembl gene identifier (e.g., ENSG00000000003) based on Ensembl release 109 and genome build 38.
`token_id`	An integer token ID used to represent each gene. This is the ID used in the `genes` field in the main data.

Cell Line Metadata

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python

cell_line_metadata = load_dataset("tahoebio/EmeraldBay", "cell_line_metadata", split="train")

Driver-mutation annotations for the 52 EmeraldBay cell lines. This is a subset of the Tahoe-100M `cell_line_metadata` table filtered to the EmeraldBay cell-line panel; the schema is preserved verbatim. The table has multiple rows per cell line (one per curated driver mutation; 1–51 rows per line, mean ~9). Join on Cell_ID_Cellosaur to match the cell_line field in expression_data and summary_statistics.

Column Name	Description
`cell_name`	Standard name of the cancer cell line (e.g., A549).
`Cell_ID_DepMap`	Unique identifier for the cell line in the DepMap project (e.g., ACH-000681).
`Cell_ID_Cellosaur`	Cellosaurus accession ID (e.g., CVCL_0023). Join key against `cell_line` in `expression_data` and `summary_statistics`.
`Organ`	Tissue or organ of origin for the cell line (e.g., Lung).
`Driver_Gene_Symbol`	HGNC-approved symbol of a known or putative driver gene with functional alterations in this cell line (e.g., KRAS, CDKN2A).
`Driver_VarZyg`	Zygosity of the driver variant (e.g., Hom for homozygous, Het for heterozygous).
`Driver_VarType`	Type of genetic alteration (e.g., Missense, Frameshift, Stopgain, Deletion).
`Driver_ProtEffect_or_CdnaEffect`	Specific protein or cDNA-level annotation of the mutation (e.g., p.G12S, p.Q37).
`Driver_Mech_InferDM`	Inferred functional mechanism of the mutation (e.g., LoF for loss-of-function, GoF for gain-of-function).
`Driver_GeneType_DM`	Classification of the driver gene as an Oncogene or Suppressor.

Drug Metadata

python

drug_metadata = load_dataset("tahoebio/EmeraldBay", "drug_metadata", split="train")

One row per single-drug perturbation in EmeraldBay (27 drugs; DMSO controls are excluded per the Tahoe-100M convention). Curated with Claude and validated against MedChemExpress, ClinicalTrials.gov, and PubChem. Drug-combination conditions (e.g. Adagrasib+Cetuximab) are not represented as rows here; join expression_data.drug against this table for single-drug perturbations and parse drugname_drugconc for combination treatments.

Column Name	Description
`drug`	Name of the treatment. Unique key for this table.
`targets`	Known molecular targets of the compound (gene symbol(s)).
`mutations`	Specific target mutation(s) the compound is selective for, when applicable (e.g. `KRASG12C`).
`moa-broad`	Broad classification of the compound's mechanism of action (typically "inhibitor/antagonist", "activator/agonist", or "unclear").
`moa-fine`	Specific functional MoA annotation (e.g. "RAS inhibitor", "MEK inhibitor", "Proteasome inhibitor").
`human-use`	"yes"/"no" — whether the compound is approved for human use.
`clinical-trials`	"yes"/"no" — whether the compound has been evaluated in any registered clinical trials.
`claude-notes-approval`	Contextual notes on the compound's approval status / clinical usage, generated by Claude.
`pubchem-cid`	PubChem Compound Identifier.
`canonical-smiles`	Canonical SMILES string representing the molecular structure (null for antibody drugs).

Sensitivity Readout

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python

summary_statistics = load_dataset("tahoebio/EmeraldBay", "summary_statistics", split="train")

Per-(cell line, condition) growth-rate summary statistics: 4,992 rows covering 52 cancer cell lines × 93 conditions (single-drug, drug-combination, and DMSO_T0 time-zero controls). This is the raw summary table; downstream loaders typically drop DMSO_T0, exclude multi-drug conditions, and mean-aggregate replicates per (cell line, condition).

Column Name	Description
`cell_line`	Cellosaurus ID of the cancer cell line (e.g., `CVCL_0023`).
`condition`	Compound × concentration, e.g. `[('Encorafenib', 0.1, 'uM')]`. May contain multiple tuples for combination treatments, and `DMSO_T0` marks time-zero vehicle controls.
`growth_rate`	Scalar growth-rate response of the cell line to the treatment.