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README.md

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Data set for Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

This data package contains the input data for all analyses in the manuscript Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes in a compute-friendly form. Not all of these data were used in the manuscript, but all of the data used in the manuscript are included here.

In this manuscript, we used hiPSC-derived cardiomyocytes as a model system for studying the relationship between transcript abundance and cellular organization as shown below. fig1

Overview

Notably, we provide 2,911 fields of view (FOVs) containing segmented single cells in different stages of cardiomyogenesis. There are 1,215 FOVs from RNA-FISH experiments (FISH; 12,941 cells) and 1,696 FOVs of live imaged cardiomyocytes (Live; 18,045 cells). The following channels were imaged:

  • Brightfield
  • Hoechst nuclear stain
  • Endogenously GFP-tagged alpha-actinin-2 structure
  • Two FISH probes per cell (FISH FOVs only; 18 probes overall)

Also included are

  • expert scoring of sarcomere structure organization of 6,677 cells (5,755 scored cells from FISH; 922 scored cells from Live)

Organization

The data in this package is organized into separate data sets, reflecting different data of different types (FISH/Live image data), and different downstream processing / feature derivation.

The data sets included in this package are:

Raw 3D images:

   raw_images
   ├──FISH 
   ├──Live

FISH 2D segmented cells

   ├──2d_segmented_fields_fish_1 
   ├──2d_segmented_fields_fish_2
   ├──2d_segmented_fields_fish_3
   ├──2d_segmented_fields_fish_4

FISH 2D FOVs used as input to cellprofiler

   ├──2d_autocontrasted_fields_and_single_cells_fish_1
   ├──2d_autocontrasted_fields_and_single_cells_fish_2
   ├──2d_autocontrasted_fields_and_single_cells_fish_3
   ├──2d_autocontrasted_fields_and_single_cells_fish_4

Cellprofiler output

   ├──2d_autocontrasted_single_cell_features_fish_1
   ├──2d_autocontrasted_single_cell_features_fish_2
   ├──2d_autocontrasted_single_cell_features_fish_3
   ├──2d_autocontrasted_single_cell_features_fish_4

Structure classifier

   ├──automated_local_and_global_structure_fish_1
   ├──automated_local_and_global_structure_fish_2
   ├──automated_local_and_global_structure_fish_3
   ├──automated_local_and_global_structure_fish_4
   ├──automated_local_and_global_structure_live

Cell features used to make manuscript figures

   revised_manuscript_plots
   ├──data.csv

The data creation and processing pipeline is organized according to the following schematic: Data pipeline schematic

Access

The data are programmatically accessible via quilt, and is also (somewhat) browse-able via this web ui.

Bulk download

To download the entire data set, install the quilt python package using

pip install quilt

and then

import quilt3
b = quilt3.Bucket("s3://allencell")
b.fetch("aics/integrated_transcriptomics_structural_organization_hipsc_cm/", "./")

Download specific files or data sets

To download only certain individual files, navigate the web ui here to the specific file you are interested in, and use the DOWNLOAD FILE button in the upper right of the page.

To download specific folders/directories of data, similarly use the web ui to find the directory you want, and check the <> CODE tab at the top of the page for the python code that downloads that specific subset of data.

Programmatic access

To access the data via the python quilt API, install quilt via pip, and then load the package with:

pkg = quilt3.Package.browse(
    "aics/integrated_transcriptomics_structural_organization_hipsc_cm",
    "s3://allencell",
)

Instructions for interacting with quilt packages in Python can be found here.

Citation

@article{Gerbin2021,
    author = {Gerbin, K. A. and Grancharova, T. and Donovan-Maiye, R. M. and Hendershott, M. C. and Anderson, H. G. and Brown, J. M. and Chen, J. and Dinh, S. Q. and Gehring, J. L. and Johnson, G. R. and Lee, H. and Nath, A. and Nelson, A. M. and Sluzewski, M. F. and Viana, M. P. and Yan, C. and Zaunbrecher, R. J. and Cordes Metzler, K. R. and Gaudreault, N. and Knijnenburg, T. A. and Rafelski, S. M. and Theriot, J. A. and Gunawardane, R. N.},
    title = {Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes},
    journal = {Cell Syst},
    volume = {12},
    number = {6},
    pages = {670-687 e10},
    ISSN = {2405-4720 (Electronic)
    2405-4712 (Linking)},
    DOI = {10.1016/j.cels.2021.05.001},
    url = {https://doi.org/10.1016/j.cels.2021.05.001},
    year = {2021},
    type = {Journal Article}
}

License

For questions on licensing please refer to https://www.allencell.org/terms-of-use.html.

Contact

Allen Institute for Cell Science E-mail: cells@alleninstitute.org

Feedback

Feedback on benefits and issues you discovered while using this data package is greatly appreciated. Feedback Form