GDPx1

GDPx1 Functional Genomics Dataset: DRUG-seq + Chemical Perturbation in A549 Cells

Experimental Design

The Library of Pharmacologically Active Compounds (LOPAC 1280), containing 1,264 compounds, was tested at two concentrations (100 nM and 1000 nM) using four technical replicates in A549 cells (a human lung carcinoma epithelial cell line). DMSO was used as an inert control, and Digitonin as a transcriptional control. This generated 28 384-well plates that were harvested after 24 hours of exposure to the compounds or DMSO controls for downstream transcriptomic analysis using Ginkgo’s custom DRUG-seq pipeline.

Metadata - metadata.csv

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

Column	Type	Example	Description
sequenced_id	int	98835510	Unique ID of the sample (well) prepared for sequencing
container_id	int	1571275	Unique ID of the sequencing library plate. The same plate organization was preserved from perturbing cells with compounds to cell lysis and library preparation.
column_id	int	20	Column position in the sequencing library plate
row_id	int	15	Row position in the plate submitted for sequencing library plate
is_edge	boolean	FALSE	Whether a sample is in a well touching the border of the sequencing library plate
compound	int	Theobromine	Name of compound used to perturb cells
compound_concentration	float	100	Compound concentration
compound_concentration_unit	string	uM	Compound concentration unit of measure
cell_line	string	A549	Cell line name
timepoint	int	24	Time between perturbation and lysis in hours
condition	string	Caffeine-100	Combination of cell line, compound, concentration, and timepoint, omitting invariate columns within an experiment, to help group replicates.
percent_volume_dmso	float	0.0625	Concentration of DMSO in perturbation sample, in percent volume. Compounds are dispensed dissolved in DMSO.
sample_type	string	Ginkgo Neg Control - DMSO	Kind of sample, either "library" or the name of a control
is_neg_control	boolean	FALSE	Whether a sample is considered a negative control
is_pos_control	boolean	TRUE	Whether a sample is considered a positive control
seeded_cell_count	int	3000	Count of cells seeded prior to perturbation
total_sequenced_reads	int	1769838	Total reads attributed to this sample
total_umi_count	int	590647	Total Unique Molecule Identifier (UMI) count
sequencing_saturation	float	0.666	Sequencing saturation, calculated as 1 - (total_umi_count/total_sequenced_reads)
ngenes3	int	6860	Count of genes with at least three UMIs
n_mapped	int	386870	Count of UMIs mapped to annotated genes
percent_mapped	float	65.5	Percent of UMIs mapped to the reference, calculated by dividing n_mapped by total_umi_count
percent_rrna_removed	float	41.77	Percent of UMIs attributed to rRNA and removed
percent_mitochondrial	float	13.58	Percent of UMIs attributed to mitochondria RNA and removed

Gene Counts - gene_counts.parquet

Gene-level UMI counts for each sample were obtained following rRNA removal (bbduk), STAR alignment (STAR) against hg38, deduplication using umi-tools, and counting with featureCounts. Columns headers represent sequenced sample IDs (sequenced_id in metadata table) and rows are genes.