inDrops-2: A flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples Journal Article
| Authors: | Juzenas, S.; Goda, K.; Kiseliovas, V.; Zvirblyte, J.; Quintinal-Villalonga, A.; Siurkus, J.; Nainys, J.; Mazutis, L. |
| Article Title: | inDrops-2: A flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples |
| Abstract: | The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples. Moreover, as the scale of single-cell sequencing continues to expand, accommodating diverse workflows and cost-effective multi-biospecimen profiling becomes more critical. Herein, we present inDrops-2, an open-source scRNA-seq technology designed to profile live or preserved cells with a sensitivity matching that of state-of-the-art commercial systems but at a 6-fold lower cost. We demonstrate the flexibility of inDrops-2, by implementing two prominent scRNA-seq protocols, based on exponential and linear amplification of barcoded-complementary DNA, and provide useful insights into the advantages and disadvantages inherent to each approach. We applied inDrops-2 to simultaneously profile multiple human lung carcinoma samples that had been subjected to cell preservation, long-term storage and multiplexing to obtain a multiregional cellular profile of the tumor microenvironment. The scalability, sensitivity and cost efficiency make inDrops-2 stand out among other droplet-based scRNA-seq methods, ideal for large-scale studies on rare cell molecular signatures. © The Author(s) 2025. |
| Keywords: | controlled study; human cell; genetics; quality control; cell viability; reverse transcription polymerase chain reaction; gene amplification; gene expression; lung neoplasms; ph; pathology; cell line, tumor; cost effectiveness analysis; economics; lung tumor; in situ hybridization; algorithm; messenger rna; microfluidics; tumor cell line; lung carcinoma; monocyte; sequence analysis, rna; room temperature; encapsulation; peripheral blood mononuclear cell; complementary dna; rna extraction; microfluidic analytical techniques; tumor microenvironment; cell composition; single cell analysis; single-cell analysis; cell encapsulation; rna-seq; procedures; hydrogel; high throughput sequencing; high-throughput nucleotide sequencing; microfluidic analysis; humans; human; article; rna sequencing; single cell rna seq; k-562 cell line; high throughput analysis; single-cell gene expression analysis |
| Journal Title: | Nucleic Acids Research |
| Volume: | 53 |
| Issue: | 2 |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Date Published: | 2025-01-27 |
| Start Page: | gkae1312 |
| Language: | English |
| DOI: | 10.1093/nar/gkae1312 |
| PUBMED: | 39797728 |
| PROVIDER: | scopus |
| PMCID: | PMC11724362 |
| DOI/URL: | |
| Notes: | Article -- MSK author Alvaro Quintanal-Villalonga's last name is misspelled on the original publication -- Source: Scopus |
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