CryoSCAPE

Abstract

The field of single cell technologies has rapidly advanced our comprehension of the human immune system, offering unprecedented insights into cellular heterogeneity and immune function. While cryopreserved peripheral blood mononuclear cell (PBMC) samples enable deep characterization of immune cells, challenges in clinical isolation and preservation limit their application in underserved communities with limited access to research facilities. We present CryoSCAPE (Cryopreservation for Scalable Cellular And Proteomic Exploration), a scalable method for immune studies of human PBMC with multi-omic single cell assays using direct cryopreservation of whole blood. This method, optimized for scalability and cost-effectiveness, allows for high-throughput single cell sequencing and functional assays while addressing sample handling challenges in the clinic. Comparative analyses and functional assays of human PBMC from cryopreserved whole blood demonstrate the efficacy of this methodology in capturing cell proportions and molecular features, showcasing its potential to democratize access to single-cell assays and enhance our understanding of immune function across diverse populations.

Figure 1

Preprocessing Inputs:

• SAMN41788226 Cell by Gene matrices CSVs RNA and ADT data, scrublet CSV to label doublets

Preprocessing Outputs:

• SAMN41788226 RDS file for use in plotting

Figure 2

A, B, C

Inputs : Preprocessing Inputs:

• SAMN41788227 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788227 RDS files for use in plotting

D

Inputs :

• Preprocessing Inputs:
• SAMN41788228 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788228 RDS files for use in plotting

E

Inputs :

• Preprocessing Inputs:
• SAMN41788229 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788229 RDS files for use in plotting

Figure 3

Preprocessing Inputs:

• SAMN41788230 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788230 RDS files for use in plotting

Figure 4

Inputs :
Preprocessing Inputs:

• SAMN41788231 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788231 RDS files for use in plotting

Figure 5

Inputs :
Preprocessing Inputs:

• SAMN41788232 H5ad files and Scrublet CSV file to label doublets

Preprocessing Outputs:

• SAMN41788232 RDS files for use in plotting