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import streamlit as st |
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st.set_page_config(layout="wide") |
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st.markdown( |
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""" |
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# Deep Learning Based Models for Preimplantation Mouse and Human Embryos Based on Single Cell RNA Sequencing |
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_[Martin Proks](https://orcid.org/0000-0002-8178-3128)\*, |
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[Nazmus Salehin](https://orcid.org/0000-0002-8155-4296)\*, |
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[Joshua M. Brickman](https://orcid.org/0000-0003-1580-7491)**_ |
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_\* There authors contributed equally to the work_ |
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_** Corresponding author [[email protected]](mailto:[email protected])_ |
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The rapid growth of single-cell transcriptomic technology has produced an increasing number of |
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datasets for both embryonic development and _in vitro_ pluripotent stem cell derived models. |
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This avalanche of data surrounding pluripotency and the process of lineage specification has |
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meant it has become increasingly difficult to define specific cell types or states and compare |
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these to _in vitro_ differentiation. Here we utilize a set of deep learning (DL) tools to |
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integrate and classify multiple datasets. This allows for the definition of both mouse and |
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human embryo cell types, lineages and states, thereby maximising the information one can garner |
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from these precious experimental resources. Our approaches are built on recent initiatives for |
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large scale human organ atlases, but here we focus on the difficult to obtain and process |
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material that spans early mouse and human development. We deploy similar approaches as the |
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initiatives building large reference organ atlases, however with a focus on early mammalian |
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development. Using publicly available data for these stages, we test different deep learning |
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approaches and develop a model to classify cell types in an unbiased fashion at the same time as |
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defining the set of genes used by the model to identify lineages, cell types and states. We have |
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used our models trained on _in vivo_ development to classify pluripotent stem cell models for |
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both mouse and human development, showcasing the importance of this resource as a dynamic |
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reference for early embryogenesis. |
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""" |
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) |
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st.image( |
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"static/Fig-1.v4.3.png", |
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caption=""" |
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Summary of datasets used to build reference models. a) Schematic overview of mouse |
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and human preimplantation development. b) Quantification of cells per publication which |
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were collected for building the mouse (grey) and human (black) reference. c) Computational |
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schematic of tools used to build and interpret the reference models. d) Gene expression |
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of canonical markers for each developmental stage in mouse (top) and human (bottom) |
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preimplantation. e) Reduced dimensional representation of preimplantation mouse (left) |
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and human (right) datasets. dpf: days post fertilization, E: embryonic day. |
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""", |
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) |
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