ALLEN CELL EXPLORER
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  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
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      3. Deep cell zoom (216,016 cells)
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      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
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      2. AGAVE 3D pathtrace image viewer
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      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
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Videos & Tutorials Collected

A comprehensive list of instructional videos & written tutorials collected from each menu category

Cell Shorts
mini-documentaries on the use & impact of hiPS cells in labs around the world

Cell Shorts:
A common platform for human cell research
Bruce Conklin from the Gladstone Institutes created WTC: a widely used human induced pluripotent stem cell line. The Allen Institute for Cell Science uses this line in the Allen Cell Collection: the first publicly available collection of gene edited, fluorescently tagged human induced pluripotent stem cells. See how the Conklin lab is using these gene edited cells to find therapies for life threatening human genetic diseases.
Cell Shorts:
Illuminating the kidney
In our new video series Cell Shorts, see how researcher Beno Freeman and his colleagues at the University of Washington are using the Allen Institute for Cell Science’s publicly available human induced pluripotent stem cells to study kidney disease and regeneration.
The Cell Catalog contains our completed cell lines, which are available through Coriell as part of the Allen Cell Collection. Click a cell line on the first page of the Cell Catalog to opens pages with supplemental material (data, images, videos) related to the rigorous testing and quality control steps each line has undergone.
Allen Cell Catalog
More videos to come..

Allen Cell Methods
Instructional Videos for Success in the Lab

To ensure researchers have success working with our human induced pluripotent stem cell lines in their lab, researchers from our teams highlight nuanced techniques and helpful tips while demonstrating various laboratory protocols.
Read our paper on Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization in Molecular Biology of the Cell (MBoC).
Visit PUBLICATIONS to download MBoC paper
ALLEN CELL METHODS
1. Thawing hiPSCs
Jacqueline Smith highlights nuanced techniques and helpful tips while demonstrating how to thaw a vial of our human gene-edited induced pluripotent stem cells.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
ALLEN CELL METHODS
2. Culturing & maintaining hiPSCs
Amanda Haupt, demonstrates our single cell passaging protocol for gene editing human induced pluripotent stem cells.
​

This process should take 15–30 minutes to complete and we recommend passaging a maximum of two cell lines at a time in parallel. Researchers can obtain our publicly available gene-edited fluorescently tagged cell lines through our Allen Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
ALLEN CELL METHODS
3. Gene editing: RNP transfection for gene-editing hiPSCs
Maggie Fuqua demonstrates our RNP transfection protocol for gene editing human induced pluripotent stem cells.

​This process should take 30–60 minutes to complete. We recommend preparing all reagents and materials beforehand. Our researchers have used the RNP transfection method for all of the gene-edited hiPS cells available through our Allen Cell Catalog.
Cell catalog to obtain plasmids
Detailed written protocols
JOVE VIDEO JOURNAL
4. Gene editing: Endogenous Protein Tagging in hiPSCs Using CRISPR/Cas9
This Jove Video Journal article presents a protocol we developed for tagging endogenously expressed proteins with fluorescent tags in human induced pluripotent stem cells using CRISPR/Cas9. Putatively edited cells are enriched by fluorescence activated cell sorting and clonal cell lines are generated.

​Access more information detailing our scientific methods & standard operating procedures. Researchers can obtain these hiPS cells or plasmids through our Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
​ALLEN CELL METHODS
5. Cardiomyocyte Differentiation of hiPSCs
Angel Nelson highlights nuanced techniques and helpful tips while demonstrating our cardiac differentiation protocol for the WTC parental line and our gene-edited cells.

If the experiment is successful, you can expect to see beating cardiomyocytes at day 7. Researchers can obtain the hiPS cells used in this protocol through our Allen Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
​ALLEN CELL METHODS
6. Techniques while working with Matrigel
Angel Nelson highlights nuanced techniques and helpful tips while working with Matrigel.

Researchers can obtain the hiPS cells used in this protocol through our Allen Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
​ALLEN CELL METHODS
7. Cryopreservation of clonal human iPS cell lines in 96-well plates
To ensure researchers have success working with our human induced pluripotent stem cell lines in their lab, our Amanda Haupt highlights helpful tips while demonstrating how to cryopreserve clonal human induced pluripotent stem cells in 96-well plates.

Researchers can obtain the hiPS cells used in this protocol through our Allen Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
 
​ALLEN CELL METHODS
8. Automated tissue culture platform
To ensure researchers have success working with our human induced pluripotent stem cell lines in their lab, our Mackenzie Coston showcases the automated tissue culture platform we use to seed, passage, feed, and maintain our cells.​

Researchers can obtain the hiPS cells used in this protocol through our Allen Cell Catalog.
Cell catalog to obtain hiPS cell lines
Detailed written protocols
 
 

Allen Cell Explorer Tutorials
Learn how to use tools & data freely available here on allencell.org

​Allen Cell Tutorials:
Navigating the Cell Catalog
Amanda Haupt represents the gene-editing team to walks you through the cell lines and supporting data available in the Allen Cell Catalog, and how to obtain the lines for use in your labs.
The Cell Catalog contains our completed cell lines, which are available through Coriell as part of the Allen Cell Collection. Click a cell line on the first page of the Cell Catalog to opens pages with supplemental material (data, images, videos) related to the rigorous testing and quality control steps each line has undergone.
Allen Cell Catalog
​Allen Cell Tutorials:
Navigating the 3D Cell Viewer
​Megan Riel-Mehan represents the Animated Cell group to present an overview of several major upgrades and an easier to use interface for the 3D Cell Viewer tool.

The 3D Cell Viewer is a tool in the Allen Cell Explorer for viewing thousands of 3D images of cellular structures and organelles.
More videos to come..

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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
  • 🔍
      SEARCHBAR