---
language:
- en
license_name: cc-by-with-restrictions
license_link: LICENSE.md
pretty_name: GDPx2
tags:
- biology
size_categories:
- 10K<n<100K
configs:
 - config_name: metadata
   data_files:
   - split: train
     path: metadata.csv
extra_gated_fields:
  First name: text
  Last name: text
  Company: text
  Work email: text
  I want to use this dataset for: text
---

# GDPx2

GDPx2 Functional Genomics Dataset: DRUG-seq + Chemical Perturbation in 4 Primary Cell Types. This dataset contains the supplementary data for the bioRxiv preprint "[Mapping the Transcriptional Landscape of Drug Responses in Primary Human Cells Using High-Throughput DRUG-seq](https://doi.org/10.1101/2025.06.03.657593)".

## Experimental Design

Experiments were performed in a 384-well format assay. Four primary human cell lines were used: aortic smooth muscle cells, skeletal myoblasts, dermal fibroblasts, and epithelial melanocytes. 85 compounds were tested at 6 concentrations (3000, 900, 300, 95, 28.5, and 9.5 nM) using four replicates for each concentration. DMSO was used as an inert control added to different volumes (0.625%, 0.1875%, 0.0625%) to match the final DMSO concentrations found in compound-treated wells. Dexamethasone, Trichostatin A, and Brefeldin A were used as transcriptional controls. This generated a total of eight 384-well plates per cell line that were harvested for downstream transcriptomic analysis after 24 hours of exposure to the compounds or DMSO controls.

## Metadata - `metadata.csv`

File with sample-level annotations and sample-level quality control metrics. The metadata table has the following fields:

| Column                        | Type      | Description                                                                                                                                                                      |
|:------------------------------|:----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `sample_id`                   | `int`     | Unique ID of the sample (well) prepared for sequencing                                                                                                                           |
| `container_id`                | `int`     | Unique ID of the perturbation or sequencing library plate. The same plate organization was preserved from perturbing cells with compounds to cell lysis and library preparation. |
| `column_id`                   | `int`     | Column position in the plate                                                                                                                                                     |
| `row_id`                      | `int`     | Row position in the plate                                                                                                                                                        |
| `analysis_id`                 | `int`     | Unique ID of the primary analysis presented for this sample. This key is used for data upload and can be ignored.                                                                |
| `is_edge`                     | `boolean` | Whether a sample is in a well touching the border of the sequencing library plate                                                                                                |
| `compound`                    | `string`  | Name of compound used to perturb cells                                                                                                                                           |
| `compound_concentration`      | `float`   | Compound concentration                                                                                                                                                           |
| `compound_concentration_unit` | `string`  | Compound concentration unit of measure                                                                                                                                           |
| `cell_line`                   | `string`  | Cell line name                                                                                                                                                                   |
| `timepoint`                   | `int`     | Time between perturbation and lysis in hours                                                                                                                                     |
| `condition`                   | `string`  | Combination of cell line, compound, concentration, and timepoint, omitting invariate columns within an experiment, to help group replicates.                                     |
| `percent_volume_dmso`         | `float`   | Concentration of DMSO in perturbation sample, in percent volume. Compounds are dispensed dissolved in DMSO.                                                                      |
| `sample_type`                 | `string`  | Kind of sample, either "library" or the name of a control                                                                                                                        |
| `is_neg_control`              | `boolean` | Whether a sample is considered a negative control                                                                                                                                |
| `is_pos_control`              | `boolean` | Whether a sample is considered a positive control                                                                                                                                |
| `seeded_cell_count`           | `int`     | Count of cells seeded prior to perturbation                                                                                                                                      |
| `total_sequenced_reads`       | `int`     | Total reads attributed to this sample                                                                                                                                            |
| `total_umi_count`             | `int`     | Total Unique Molecule Identifier (UMI) count                                                                                                                                     |
| `sequencing_saturation`       | `float`   | Sequencing saturation, calculated as `1 - (total_umi_count/total_sequenced_reads)`                                                                                               |
| `ngenes3`                     | `int`     | Count of genes with at least three UMIs                                                                                                                                          |
| `n_mapped`                    | `int`     | Count of UMIs mapped to annotated genes                                                                                                                                          |
| `percent_mapped`              | `float`   | Percent of UMIs mapped to the reference, calculated by dividing `n_mapped by` `total_umi_count`                                                                                  |
| `percent_rrna_removed`        | `float`   | Percent of input reads attributed to rRNA and removed                                                                                                                            |
| `percent_mitochondrial`       | `float`   | Percent of UMIs attributed to mitochondria RNA                                                                                                                                   |
| `unassigned_multimapping`     | `int`     | Number of reads that could not be uniquely assigned to a single gene due to mapping to multiple genes                                                                            |
| `unassigned_nofeatures`       | `int`     | Number of reads that could not be assigned to any gene                                                                                                                           |
| `percent_duplicated`          | `float`   | Percentage of reads that are UMI duplicates                                                                                                                                      |

## Compound Library - `compound_library.csv`

Additional information about the compounds tested.

| Column     | Type     | Description                                          |
|:-----------|:---------|:-----------------------------------------------------|
| `Drug`     | `string` | Name of the compound                                 |
| `Type`     | `string` | "positive control", "negative control", or "library" |
| `Category` | `string` | Functional category of the compound                  |
| `Function` | `string` | Function of the compound                             |

## Gene Counts - `gene_counts.parquet`

Gene-level UMI counts for each sample were obtained following rRNA removal ([bbduk](https://archive.jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)), STAR alignment ([STAR](https://github.com/alexdobin/STAR)) against hg38, deduplication using [umi-tools](https://github.com/CGATOxford/UMI-tools), and counting with [featureCounts](https://subread.sourceforge.net/featureCounts.html). Columns headers represent sequenced sample IDs (`sequenced_id` in metadata table) and rows are genes. See methods section 4.3 in the [pre-print](https://doi.org/10.1101/2025.06.03.657593) for more details.

## Differential Expression - `differential_expression.parquet`

Differentially expressed genes were identified using DESeq2, comparing each treatment (compound at a specific concentration) to DMSO controls with matched DMSO concentration on the same plate. See methods section 4.4 in the [pre-print](https://doi.org/10.1101/2025.06.03.657593) for more details.

| Column           | Type      | Description                                                                                                                                                                                                                                                     |
|:-----------------|:----------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `cell_line`      | `string`  | Cell line or cell type                                                                                                                                                                                                                                          |
| `compound`       | `string`  | Compound name                                                                                                                                                                                                                                                   |
| `concentration`  | `numeric` | Compound concentration in nM                                                                                                                                                                                                                                    |
| `gene`           | `string`  | Gene symbol                                                                                                                                                                                                                                                     |
| `baseMean`       | `numeric` | baseMean value computed by DESeq2, corresponding to the average of normalized counts across samples treated with a particular concentration of compound and the matched DMSO control samples (see Methods)                                                      |
| `log2FoldChange` | `numeric` | log2FoldChange value computed by DESeq2, corresponding to the base-2 logarithm of the normalized count fold change between samples treated with a particular concentration of compound and matched DMSO control samples, after applying shrinkage (see Methods) |
| `lfcSE`          | `numeric` | lfcSE value computed by DESeq2, corresponding to the standard error of the log2FoldChange estimate (see Methods)                                                                                                                                                |
| `pvalue`         | `numeric` | pvalue computed by DESeq2 representing the statistical significance of the observed differential expression (see Methods)                                                                                                                                       |

## Cluster Memberships - `cluster_memberships.csv`

Cluster Memberships- Identify of compounds belonging to clusters identified by Canonical Correlation Analysis. See methods section 4.6 in the [pre-print](https://doi.org/10.1101/2025.06.03.657593) for more details.

| Column                         | Type      | Description                                                                                                                                                                   |
|:-------------------------------|:----------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `cell_line`                    | `string`  | Cell line or cell type                                                                                                                                                        |
| `compound`                     | `string`  | Compound name                                                                                                                                                                 |
| `concentration`                | `numeric` | Compound concentration in nM                                                                                                                                                  |
| `sample_id`                    | `numeric` | Sample ID                                                                                                                                                                     |
| `cluster`                      | `numeric` | Cluster number (0-based)                                                                                                                                                      |
| `majority_cluster`             | `numeric` | Majority cluster for all samples with the same combination of `cell_line`, `compound`, and `concentration`. In case of a tie, the first cluster in numerical order is chosen. |
| `fraction_in_majority_cluster` | `numeric` | Fraction of samples sharing the same combination of `cell_line`, `compound`, and `concentration` belonging to the `majority_cluster`                                          |

## Dose Response - `dose_response.parquet`

Genes showing dose-dependent gene expression changes identified based on logistic-regression. See methods section 4.7 in the [pre-print](https://doi.org/10.1101/2025.06.03.657593) for more details.

| Column                                | Type      | Description                                                                                                                                                                                                                                                      |
|:--------------------------------------|:----------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `cell_line`                           | `string`  | Cell line or cell type                                                                                                                                                                                                                                           |
| `compound`                            | `string`  | Compound name                                                                                                                                                                                                                                                    |
| `gene`                                | `string`  | Gene symbol                                                                                                                                                                                                                                                      |
| `log2fc_min`                          | `numeric` | Minimum log2FoldChange calculated by DESeq2 across all compound concentrations (see Methods)                                                                                                                                                                     |
| `log2fc_max`                          | `numeric` | Maximum log2FoldChange calculated by DESeq2 across all compound concentrations (see Methods)                                                                                                                                                                     |
| `fit_alpha`                           | `numeric` | Fitted value computed by drda for the alpha parameter of the 4-parameter logistic model (see Methods)                                                                                                                                                            |
| `fit_delta`                           | `numeric` | Fitted value computed by drda for the delta parameter of the 4-parameter logistic model computed by drda (see Methods)                                                                                                                                           |
| `fit_eta`                             | `numeric` | Fitted value computed by drda for the eta parameter of the 4-parameter logistic model (see Methods)                                                                                                                                                              |
| `fit_phi`                             | `numeric` | Fitted value computed by drda for the phi parameter of the 4-parameter logistic model (see Methods)                                                                                                                                                              |
| `fit_anova_model1_aic`                | `numeric` | Akaike Information Criterion computed by drda for the 1-parameter (i.e., horizontal line) model (see Methods)                                                                                                                                                    |
| `fit_anova_model2_aic`                | `numeric` | Akaike Information Criterion computed by drda for the 4-parameter logistic model (see Methods)                                                                                                                                                                   |
| `fit_anova_model2_vs_model1_pval`     | `numeric` | p-value of the Likelihood Ratio Test computed by drda comparing the 4-parameter logistic model to the 1-parameter model (see Methods)                                                                                                                            |
| `fit_anova_model2_vs_model1_pval_adj` | `numeric` | p-value of the Likelihood Ratio Test computed by drda comparing the 4-parameter logistic model to the 1-parameter model, adjusted for multiple testing by cell line and compound using the Bonferroni-Hochberg procedure (see Methods)                           |
| `pass_complete_series`                | `boolean` | Whether all compound concentrations have a non-NA shrunken log2FoldChange computed by DESeq2 (see Methods)                                                                                                                                                       |
| `pass_robust_log2fc`                  | `boolean` | Whether at least one of DESeq2-computed log2FoldChange values is greater than 1 for genes with positive slope or lower than -1 for genes with negative slope, with the slope sign derived from the fitted delta parameter of the logistic function (see Methods) |
| `pass_aic`                            | `boolean` | Whether the 4-parameter logistic model provides a better fit than a horizontal line according to the Akaike Information Criterion (see Methods)                                                                                                                  |
| `pass_lrt`                            | `boolean` | Whether the p-value from the Likelihood Ratio Test comparing the 4-parameter to the 1-parameter model, adjusted for multiple testing, is less than 0.05 (see Methods)                                                                                            |
| `is_dose_dependent`                   | `boolean` | Whether all four criteria above are met (see Methods)                                                                                                                                                                                                            |

## GSEA - `gsea_hallmark_genes.csv` & `gsea_hdac_inhibitors.csv`

Gene set enrichment analysis results for each treatment identified by ClusterProfiler. See methods section 4.6 in the [pre-print](https://doi.org/10.1101/2025.06.03.657593) for more details.

| Column                         | Type      | Description                                                                                                                                                                                                                                                                                                                                                                                                                                       |
|:-------------------------------|:----------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `cell_line`                    | `string`  | Cell line or cell type                                                                                                                                                                                                                                                                                                                                                                                                                            |
| `gene_set_id`                  | `string`  | Gene set ID                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| `compound`                     | `string`  | Compound name                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| `concentration`                | `numeric` | Compound concentration in nM                                                                                                                                                                                                                                                                                                                                                                                                                      |
| `majority_cluster`             | `numeric` | Majority cluster for all samples with the same combination of `cell_line`, `compound`, and `concentration`. In case of a tie, the first cluster in numerical order is chosen.                                                                                                                                                                                                                                                                     |
| `fraction_in_majority_cluster` | `numeric` | Fraction of samples sharing the same combination of `cell_line`, `compound`, and `concentration`belonging to the `majority_cluster`                                                                                                                                                                                                                                                                                                              |
| `setSize`                      | `numeric` | setSize computed by ClusterProfiler's GSEA function, corresponding to the number of genes in the gene set (see Methods)                                                                                                                                                                                                                                                                                                                           |
| `enrichmentScore`              | `numeric` | enrichmentScore (ES) computed by ClusterProfiler's GSEA function, reflecting the gene set overrepresentation at the top (positive enrichment scores) or bottom (negative enrichment scores) of the list of genes in DRUG-seq data, ranked by decreasing shrunken log2FoldChange (see Methods)                                                                                                                                                     |
| `NES`                          | `numeric` | Normalized Enrichment Score (NES) computed by ClusterProfiler's GSEA function, accounting for differences in gene set size and in correlations between gene sets and DRUG-seq data (see Methods)                                                                                                                                                                                                                                                  |
| `pvalue`                       | `numeric` | pvalue computed by ClusterProfiler's GSEA function, representing the statistical significance of the enrichment score (see Methods)                                                                                                                                                                                                                                                                                                               |
| `p.adjust`                     | `numeric` | p.adjust computed by ClusterProfiler's GSEA function, representing the statistical significance of the enrichment score adjusted for multiple testing across gene sets (see Methods)                                                                                                                                                                                                                                                              |
| `qvalue`                       | `numeric` | qvalue computed by ClusterProfiler's GSEA function (see Methods), estimating the false discovery rate for the normalized enrichment score (see Methods)                                                                                                                                                                                                                                                                                           |
| `rank`                         | `numeric` | rank computed by ClusterProfiler's GSEA function, corresponding to the position in the ranked list of genes where the maximum enrichment score occurs (see Methods)                                                                                                                                                                                                                                                                               |
| `leading_edge`                 | `string`  | Leading edge metrics computed by ClusterProfiler's GSEA function. "Tags" is the percentage of gene hits before the enrichment score peak for positive ES,  or after the peak, for negative ES. "List" is the percentage of genes in the ranked gene list before the enrichment score peak for positive ES, or after the peak for negative ES. Signal is the enrichment signal strength, combining the "tags" and "list" statistics (see Methods). |
| `core_enrichment`              | `string`  | core_enrichment computed by ClusterProfiler's GSEA function, corresponding to the list of genes found in the leading edge and, therefore, contributing the most to the enrichment signal (see Methods)                                                                                                                                                                                                                                            |