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Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity

Zhu, Qian and Shah, Sheel and Dries, Ruben and Cai, Long and Yuan, Guo-Cheng (2018) Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity. . (Submitted) http://resolver.caltech.edu/CaltechAUTHORS:20180822-140737502

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Abstract

Both the intrinsic regulatory network and spatial environment are contributors of cellular identity and result in cell state variations. However, their individual contributions remain poorly understood. Here we present a systematic approach to integrate both sequencing- and imaging-based single-cell transcriptomic profiles, thereby combining whole-transcriptomic and spatial information from these assays. We applied this approach to dissect the cell-type and spatial domain associated heterogeneity within the mouse visual cortex region. Our analysis identified distinct spatially associated signatures within glutamatergic and astrocyte cell compartments, indicating strong interactions between cells and their surrounding environment. Using these signatures as a guide to analyze single cell RNAseq data, we identified previously unknown, but spatially associated subpopulations. As such, our integrated approach provides a powerful tool for dissecting the roles of intrinsic regulatory networks and spatial environment in the maintenance of cellular states.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/275156DOIDiscussion Paper
https://bitbucket.org/qzhu/smfish-hmrfRelated ItemCode Availability
https://bitbucket.org/qzhu/smfish-hmrfRelated ItemData Availability
ORCID:
AuthorORCID
Cai, Long0000-0002-7154-5361
Additional Information:The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license. bioRxiv preprint first posted online Mar. 2, 2018. Code Availability: Code is deposited at https://bitbucket.org/qzhu/smfish-hmrf. Data Availability: Expression data, spatial coordinates, SVM prediction results and HMRF segmentation results are deposited at https://bitbucket.org/qzhu/smfish-hmrf. Animal research was conducted in compliance with all relevant ethical regulations and other institutional requirements.
Record Number:CaltechAUTHORS:20180822-140737502
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20180822-140737502
Official Citation:Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity. Qian Zhu, Sheel Shah, Ruben Dries, Long Cai, Guo-Cheng Yuan bioRxiv 275156; doi: https://doi.org/10.1101/275156
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:89047
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:22 Aug 2018 21:25
Last Modified:22 Aug 2018 21:25

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