Data Set: Parse 10 Million Human PBMCs in a Single Experiment

October 30, 2025/in Parse/by Harshita Sharma

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Key Takeaways

Analyze 10 million cells across 1,152 samples in a single experiment
Increase statistical power by profiling more cells per sample
Capture detailed cellular responses to perturbations and drug treatments

Figure 1: Experimental Design Overview
Approximately 10 million PBMCs from 12 healthy donors were treated with 90 different cytokines in a single GigaLab experiment, covering 1,092 experimental conditions.

Cells were thawed, washed, and seeded at 1 million cells per well across 12 plates. After 24-hour cytokine treatment, cells were fixed, barcoded, and processed for whole transcriptome sequencing. Libraries were sequenced on the Ultima Genomics platform, achieving ~31,000 reads per cell, with 62.45% cell retention after barcoding.

Results?

After data processing with the Parse Analysis Pipeline v1.4.0, integration, and classification, 9,697,974 cells across 18 immune cell types were identified—including rare populations that are typically missed in smaller experiments. Each condition yielded a median of 7,400 cells, enabling high-resolution analysis of immune responses.

Differential expression analysis identified how cytokines influenced gene activity across cell types. Many cytokines triggered strong transcriptional responses, with over 50 genes upregulated per treatment.

Figure 2: Single-Cell UMAP Overview
9,697,974 PBMCs from 12 donors were integrated with Harmony, clustered using Scanpy, and manually annotated, revealing 18 immune cell types present across all donors and experimental conditions.

Figure 3: Cytokine-Induced Gene Changes
A heatmap summarizes the averaged number of genes significantly upregulated (log fold change >0.3, p <0.001) for each cell type and cytokine, highlighting which immune cells respond most strongly to specific cytokine treatments.

Example tutorial vignettes from Parse Biosciences and Fabian Theis’ lab at Helmoltz-Munich:

Parse 10M PBMC Cytokines Clustering Tutorial
Joey Pangallo, Efi Papalexi – Parse Biosciences, Seattle, WA
Step-by-step example of analyzing 10 million PBMCs treated with cytokines using the Evercode workflow. Covers data loading, preprocessing, Leiden clustering, and generating UMAP plots with Scanpy.

Parse 10M PBMC Cytokines Clustering Tutorial (Downsampled)
Joey Pangallo, Efi Papalexi – Parse Biosciences, Seattle, WA
Same workflow as above, starting with a downsampled dataset of 1 million cells. Ideal for quicker exploration or limited CPU memory setups.

scCODA Parse 10M PBMC Cytokines
Artur Szałata, Dominik Klein, Soeren Becker, Fabian Theis – Helmholtz-Munich
Demonstrates analysis of cell proportion changes across 10 million PBMCs. Shows how using the full dataset improves statistical significance of perturbation effects. Based on scCODA, a Bayesian model for compositional single-cell data analysis (Nat Commun 12, 6876, 2021).

Parse 10M PBMC Cytokines Dask Workflow
Artur Szałata, Dominik Klein, Soeren Becker, Fabian Theis – Helmholtz-Munich
Walks through preprocessing the 10M cell dataset using Dask. Loads data chunk-wise to reduce memory use and demonstrates highly variable gene selection for downstream analysis.

Dataset License: CC BY-NC 4.0 (non-commercial use). Commercial licensing inquiries: support@parsebiosciences.com

QUICK DOWNLOAD FILES

10M PBMC 12donor 90cytokines h5ad (212 GB)

Parse 10M PBMC cytokines clustering tutorial

Parse 10M PBMC cytokines clustering tutorial on downsampled data

scCODA Parse 10M PBMC cytokines

Parse 10M PBMC cytokines Dask workflow

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Evercode TCR Mega

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

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February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

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High TCR detection in activated and primary T cells

Witness exceptional TCR detection in both activated and primary T cells through our state-of-the-art profiling techniques. In our investigation, T cells sourced from peripheral blood mononuclear cells (PBMCs) underwent two distinct conditions: direct profiling (Primary) and activation via culture for 3 days with CD3/CD28 beads and IL-2 (Activated).

Our findings reveal robust TCR detection in both experimental conditions, underscoring the versatility and dependability of our methodology across various T cell states. Whether profiling primary T cells or their activated counterparts, our approach guarantees precise and comprehensive characterization of the TCR repertoire, offering invaluable insights into immune responses and cellular dynamics.

Rely on our advanced profiling techniques to deliver meticulous and high-fidelity data, facilitating a deeper comprehension of T cell biology and immunological processes. With our innovative methodologies, explore the intricacies of the immune system with confidence and clarity.

Comprehensive immune repertoire detection

Experience unparalleled detection of the immune repertoire with the Evercode™ TCR kit, designed to provide the most comprehensive profile available. In a groundbreaking study encompassing 8 donors, our kit identified nearly 500,000 unique beta chain clonotypes.

Remarkably, the vast majority of these clonotypes were classified as rare, highlighting the sensitivity and depth of our detection capabilities. With the Evercode™ TCR kit, you can uncover the full spectrum of immune diversity, from common to exceedingly rare clonotypes, empowering you to explore the intricacies of immune responses with unprecedented precision and breadth.

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Evercode TCR Mini

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

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This groundbreaking approach empowers you to uncover the intricate interplay between TCR diversity and gene expression profiles at the single-cell level, providing a comprehensive understanding of immune responses and cellular heterogeneity. Say goodbye to the limitations of traditional methods and embark on a new era of immunogenomics research with our integrated solution.

High TCR detection in activated and primary T cells

Experience high TCR detection in both activated and primary T cells with our advanced profiling techniques. In our study, T cells isolated from peripheral blood mononuclear cells (PBMCs) underwent two distinct conditions: direct profiling (Primary) and activation through culture for 3 days with CD3/CD28 beads and IL-2 (Activated).

Our results demonstrate robust TCR detection in both scenarios, showcasing the versatility and reliability of our methodology across different T cell states. Whether profiling primary T cells or activated counterparts, our approach ensures accurate and comprehensive characterization of the TCR repertoire, providing invaluable insights into immune responses and cellular dynamics.

Count on our advanced profiling techniques to deliver precise and high-quality data, enabling deeper understanding of T cell biology and immunological processes.

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February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

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February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

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February 20, 2024/in Evercode, Parse, Partners/by Harshita Sharma

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WORKS WITH FIXED CELLS AND NUCLEI

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