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Gene-edited cells
​differentiated into cardiomyocytes

Stem cells differentiated into cardiomyocytes beat spontaneously
 

Publication

Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
We present a quantitative co-analysis of RNA abundance and sarcomere organization in single cells and an integrated framework to predict subcellular organization states from gene expression. This study establishes a framework for multi-dimensional analysis of single cells to study the relationships between gene expression and subcellular organization and to develop a more nuanced description of cell states.

Cell line used in the study to produce the dataset for all analyses: ACTN2-GFP (cell line ID:
AICS-0075 cl.85) - more information about the cell line can be found on the Cell Catalog page. 
BioRxiv preprint
Dataset for all analyses
Analysis code on GitHub
GitHub notebook for figures
Graphical Abstract: Transcriptional profiling and structural classification was performed on human induced pluripotent stem cell-derived cardiomyocytes to characterize the relationship between transcript abundance and subcellular organization.
Graphical Abstract

Gene edited cells differentiate into cardiomyocytes

A. 
B. 
C. 
Figure 1. After differentiation of the edited stem cells into cardiomyocytes, cells begin to beat spontaneously. Three videos taken at day 16 of differentiation show a variety of different rates and behaviors: (A) small contractile pulsing of the tissue, which remains attached to the bottom of the culture dish. (B) Wavelike, synchronous beating throughout the cardiac tissue, which has lifted off the bottom of the culture dish in most regions in this field of view. (C) Similar wavelike beating as seen in (B), however more vigorous and at a faster rate.

Playback speed is real time and each video is roughly 2.5mm across the field of view, taken from a standard camera looking through the microscope eyepiece.
Picture
Figure 2. Many structures reorganize during differentiation. α-actinin found primarily in the rings and fiber bundles at the top and bottom of hiPSCs respectively are reorganized into the contractile apparatus of sarcomeres in cardiomyocytes.

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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
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