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Stories in Single Cell RNA Sequencing


da Veiga Beltrame, Eduardo (2022) Stories in Single Cell RNA Sequencing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4kgh-8420.


This thesis describes the projects I have worked on since starting the Caltech bioengineering program in fall 2017. The general theme of my projects is that they are all about single cell RNA sequencing (scRNA-seq), spanning the experimental and computational realms.

Chapter 1 is an introduction explaining the essential concepts and is meant to be readable by a wide audience. For the other chapters, each one describes a separate project in a succinct manner, including links to the related preprint, published paper or code repositories at the start of each chapter.

Chapter 2 describes the scVI generative model for scRNA-seq data and the scvi-tools framework, which forms the basis of many of my computational projects.

Chapter 3 describes an open source 3D printable syringe pump system that was developed envisioning facilitating many kinds of experiments, in particular droplet based scRNA-seq.

Chapter 4 describes a new way of fabricating hydrogel beads with unique DNA barcodes that are used for scRNA-seq experiments.

Chapter 5 describes a database listing most published scRNA-seq studies that I helped create, and provides a useful overview of the state of the field.

Chapter 6 describes the kallisto bus workflow, which is used for pre-processing scRNA-seq data, going from FASTQ file to gene count matrix in a very efficient manner.

Chapter 7 describes a new way of using scVI to quantify the trade- off in the quality of scRNA-seq of a given dataset when surveying more cells or sequencing more reads per cell.

Chapter 8 describes tools developed for the WormBase users to leverage scRNA-seq data on C. elegans, and which can be deployed with any other scRNA-seq dataset.

Chapter 9 describes a remarkably successful offshoot of the devel- opment of these tools: a simple scVI based analysis and visualization strategy for finding candidate marker genes using C. elegans scRNA-seq data, which was experimentally validated by members of the Sternberg lab.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:single cell RNA sequencing, bioinformatics, scRNA-seq
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Sternberg, Paul W.
Thesis Committee:
  • Thomson, Matthew (chair)
  • Pachter, Lior S.
  • Van Valen, David A.
  • Sternberg, Paul W.
Defense Date:27 October 2021
Non-Caltech Author Email:veigabeltrame (AT)
Record Number:CaltechTHESIS:06022022-201232129
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for chapter 3 adapted for chapter 5 adapted for chapter 4 adapted for chapter 7 adapted for chapter 6 adapted for chapter 8 adapted for chapter 2
da Veiga Beltrame, Eduardo0000-0002-1529-9207
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14938
Deposited By: Eduardo da Veiga Beltrame
Deposited On:02 Jun 2022 23:49
Last Modified:09 Jun 2022 19:34

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