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Isoform specificity in the mouse primary motor cortex

Booeshaghi, A. Sina and Yao, Zizhen and van Velthoven, Cindy and Smith, Kimberly and Tasic, Bosiljka and Zeng, Hongkui and Pachter, Lior (2020) Isoform specificity in the mouse primary motor cortex. . (Unpublished)

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Full-length SMART-Seq single-cell RNA-seq can be used to measure gene expression at isoform resolution, making possible the identification of gene isoform markers for cell types. In a comprehensive analysis of 6,160 mouse primary motor cortex cells assayed with SMART-Seq, we find numerous examples of isoform specificity in cell types, including isoform shifts between cell types that are masked in gene-level analysis. These findings can be used to refine spatial gene expression information to isoform resolution. Our results highlight the utility of full-length single-cell RNA-seq when used in conjunction with other single-cell RNA-seq technologies.

Item Type:Report or Paper (Discussion Paper)
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URLURL TypeDescription Paper ItemData/Code
Booeshaghi, A. Sina0000-0002-6442-4502
Yao, Zizhen0000-0002-9361-5607
van Velthoven, Cindy0000-0001-5120-4546
Smith, Kimberly0000-0002-3142-1970
Tasic, Bosiljka0000-0002-6861-4506
Zeng, Hongkui0000-0002-0326-5878
Pachter, Lior0000-0002-9164-6231
Alternate Title:Isoform cell type specificity in the mouse primary motor cortex
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Posted March 06, 2020. We thank members of the BICCN consortium, especially the “Mini-MOp” analysis group, for helpful conversations related to transcriptome analysis of the primary motor cortex. Thanks to Nadezda Volovich, Vasilis Ntranos, and Páll Melsted, for help with a preliminary quantification of the SMART-Seq data. This work was funded by the NIH Brain Initiative via grant U19MH114930 to HZ and LP). Data and Software Availability: The software used to generate the results and figures of the paper is available at . The single-cell RNA-seq data used in this study was generated as part of the BICCN consortium 17 . The 10xv3 and SMART-Seq data can be downloaded from . The MERFISH data was generated as part of the BICCN consortium but is not currently available due to restrictions by Xiaowei Zhuang; requests for the data can be made directly to her by emailing Author Contributions: ASB and LP conceived the study. ASB implemented the methods and produced the results and figures. ASB and LP analyzed the data and wrote the manuscript. ZY, CV, KS, BT and HZ produced the SMART-Seq and 10xv3 data.
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Record Number:CaltechAUTHORS:20200306-130944112
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Official Citation:Isoform specificity in the mouse primary motor cortex. A. Sina Booeshaghi, Zizhen Yao, Cindy van Velthoven, Kimberly Smith, Bosiljka Tasic, Hongkui Zeng, Lior Pachter. bioRxiv 2020.03.05.977991; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101743
Deposited By: Tony Diaz
Deposited On:06 Mar 2020 21:27
Last Modified:09 Mar 2020 17:40

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