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Open-Source Custom Beads for Single-Cell Transcriptomics


Dilanyan, Taleen Gaied (2024) Open-Source Custom Beads for Single-Cell Transcriptomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/v52p-gf80.


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.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Single-cell sequencing, Open-source Technology Development, Primer Exchange Reaction (PER), Microfluidics
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Pachter, Lior S.
Thesis Committee:
  • Rees, Douglas C. (chair)
  • Shapiro, Mikhail G.
  • Hsieh-Wilson, Linda C.
  • Pachter, Lior S.
Defense Date:25 August 2023
Non-Caltech Author Email:taleen.dilanyan (AT)
Funding AgencyGrant Number
NSF Graduate Research Fellowship2139433
Record Number:CaltechTHESIS:01162024-161326655
Persistent URL:
Dilanyan, Taleen Gaied0000-0002-3131-3259
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16280
Deposited By: Taleen Dilanyan
Deposited On:27 Mar 2024 21:41
Last Modified:03 Apr 2024 20:27

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