Open-Source Custom Beads for Single-Cell Transcriptomics

Author: Dilanyan, Taleen Gaied

Year: 2024

Degree: Dissertation (Ph.D.)

Advisor: Pachter, Lior S.

Committee Members: Rees, Douglas C.; Shapiro, Mikhail G.; Hsieh-Wilson, Linda C.; Pachter, Lior S.

Option: Chemistry

DOI: 10.7907/v52p-gf80

Abstract

Open-source single-cell genomics technologies have helped democratize single-cell genomics and expedite method development. Methods such as inDrops and Drop-seq for single-cell RNA-seq preceded popular technologies such as the 10x Genomics’ Chromium platform, however despite initial enthusiasm for open-source methods, their popularity has waned. A major reason has been the lack of availability of low-cost, customizable beads, which are essential for microfluidics based single-cell RNA-seq. We address this challenge by introducing a new method for producing barcoded hydrogel beads for single-cell RNA-seq called HiPER (High-throughput PER-barcoded hydrogel beads) that allows for increasing the diversity of barcode sequences, reducing manufacturing cost, and that can be readily adapted to custom applications. HiPER barcodes are decoupled from the capture sequences and can therefore be configured to capture RNA, DNA, or tailored for specific-gene enrichment.

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