Image-based mapping of cells onto a cell cycle continuum for integration of single cell sequencing and live cell imaging

Andrew Schultz, Saeed Alahmari, Joeseph Johnson, Thomas Veith, Zaid Siddiqui, Issam El Naqa, Laura Heiser, Noemi Andor

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Incorporation of prior information in the form of pathway activity profiles was key in the success of the algorithm that won the DREAM challenge to predict in vitro cell fitness from transcriptomic and other multi-omic datasets [1]. We hypothesize that leveraging additional prior information on the spatial distribution of transcriptome activity inside the cell will yield better predictions of cell fitness, which span longer timeframes. A prerequisite to achieve this is the ability to integrate transcriptomic and phenotypic measurements at high cellular resolution. One way to achieve this is to leverage the fact that cells sampled for both assay are in various stages of the cell cycle. ScRNA-seq provides a high temporal resolution on the cell cycle progression of sequenced cells. We show that 3D imaging of subcellular compartments can provide a comparable resolution on the cell cycle state of imaged cells. We use a method developed for scRNA-seq on size and shape statistics of subcellular compartments to assign a so-called 'pseudotime' to each imaged cell. Preliminary validation with live-cell imaging supports the hypothesis that the inferred pseudotime follows the cells' progress through the cell cycle.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE 8th International Conference on Big Data Computing Service and Applications, BigDataService 2022
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages119-123
Number of pages5
ISBN (Electronic)9781665458900
DOIs
StatePublished - 2022
Event8th IEEE International Conference on Big Data Computing Service and Applications, BigDataService 2022 - Newark, United States
Duration: Aug 15 2022Aug 18 2022

Publication series

NameProceedings - IEEE 8th International Conference on Big Data Computing Service and Applications, BigDataService 2022

Conference

Conference8th IEEE International Conference on Big Data Computing Service and Applications, BigDataService 2022
Country/TerritoryUnited States
CityNewark
Period8/15/228/18/22

Keywords

  • Data integration
  • Live-cell imaging
  • Single cell RNA sequencing
  • cell cycle
  • convolutional neural networks

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Information Systems
  • Software
  • Information Systems and Management
  • Safety, Risk, Reliability and Quality

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