An open-source platform for single-cell spatial genomics
Iain Clark, Professor
Bioengineering
Closed. This professor is continuing with Fall 2024 apprentices on this project; no new apprentices needed for Spring 2025.
This project aims to hack an Illumina HiSeqX to create an open-source sequencing platform for spatial analysis of single cells (RNA-seq, DNA-seq, etc on tissue). The HiSeqX contains advanced fluidics and optics made for Next Generation Sequencing (NGS). A community of hackers is working to repurpose these advanced instruments for scientific discovery by writing code to control the fluidics and enable new applications. Our goal is to continue this work and develop a method to sequencing DNA from single cells.
Role: Build on existing software (python) to interface with fluidics, optics, and stages and create an open-source microfluidics platform.
Qualifications: Experience with embedded systems, software engineering (python), and a desire to learn about biology.
Hours: 9-11 hrs
Off-Campus Research Site: Clark Lab 392 Stanley Hall
Related website: https://clarklab.berkeley.edu/
Related website: https://pyseq2500.readthedocs.io/en/latest/