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Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons

Alec Barrett, Erdem Varol, Alexis Weinreb, Seth R. Taylor, Rebecca M. McWhirter, Cyril Cros, Manasa Basaravaju, Abigail Poff, John A. Tipps, Maryam Majeed, Berta Vidal, Chen Wang, Eviatar Yemini, Emily A. Bayer, HaoSheng Sun, Oliver Hobert, David M. Miller III, View ORCID ProfileMarc Hammarlund
doi: https://doi.org/10.1101/2022.04.05.487209
Alec Barrett
1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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Erdem Varol
2Department of Statistics, Columbia University, New York, NY, USA
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Alexis Weinreb
1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
3Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
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Seth R. Taylor
4Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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Rebecca M. McWhirter
4Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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Cyril Cros
5Department of Biological Sciences, Columbia University, New York, NY, USA
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Manasa Basaravaju
1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
3Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
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Abigail Poff
4Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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John A. Tipps
4Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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Maryam Majeed
5Department of Biological Sciences, Columbia University, New York, NY, USA
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Berta Vidal
5Department of Biological Sciences, Columbia University, New York, NY, USA
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Chen Wang
5Department of Biological Sciences, Columbia University, New York, NY, USA
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Eviatar Yemini
6Neurobiology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Emily A. Bayer
5Department of Biological Sciences, Columbia University, New York, NY, USA
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HaoSheng Sun
7Department of Cell, Developmental, and Integrative Biology, University of Alabama, Birmingham, AL, USA
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Oliver Hobert
5Department of Biological Sciences, Columbia University, New York, NY, USA
8Howard Hughes Medical Institute, Columbia University, New York, NY, USA
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  • For correspondence: marc.hammarlund@yale.edu david.miller@vanderbilt.edu or38@columbia.edu
David M. Miller III
4Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
9Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
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  • For correspondence: marc.hammarlund@yale.edu david.miller@vanderbilt.edu or38@columbia.edu
Marc Hammarlund
1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
3Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
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  • ORCID record for Marc Hammarlund
  • For correspondence: marc.hammarlund@yale.edu david.miller@vanderbilt.edu or38@columbia.edu
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Abstract

Neuron-specific morphology and function are fundamentally tied to differences in gene expression across the nervous system. We previously generated a single cell RNA-seq dataset for every anatomical neuron class in the C. elegans hermaphrodite. Here we present a complementary set of bulk RNA-seq samples for 41 of the 118 neuron classes in C. elegans. We show that the bulk dataset captures both lowly expressed and noncoding RNAs that are missed in the single cell dataset, but also includes false positives due to contamination by other cell types. We present an integrated analytical strategy that effectively resolves both the low sensitivity of single cell RNA-seq data and the reduced specificity of bulk RNA-Seq. We show that this integrated dataset enhances the sensitivity and accuracy of transcript detection and quantification of differentially expressed genes. We propose that our approach provides a new tool for interrogating gene expression, by bridging the gap between old (bulk) and new (single cell) methodologies for transcriptomic studies. We suggest that these datasets will advance the goal of delineating the mechanisms that define neuronal morphology and connectivity in C. elegans.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
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-NC-ND 4.0 International license.
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Posted April 08, 2022.
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Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons
Alec Barrett, Erdem Varol, Alexis Weinreb, Seth R. Taylor, Rebecca M. McWhirter, Cyril Cros, Manasa Basaravaju, Abigail Poff, John A. Tipps, Maryam Majeed, Berta Vidal, Chen Wang, Eviatar Yemini, Emily A. Bayer, HaoSheng Sun, Oliver Hobert, David M. Miller III, Marc Hammarlund
bioRxiv 2022.04.05.487209; doi: https://doi.org/10.1101/2022.04.05.487209
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Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons
Alec Barrett, Erdem Varol, Alexis Weinreb, Seth R. Taylor, Rebecca M. McWhirter, Cyril Cros, Manasa Basaravaju, Abigail Poff, John A. Tipps, Maryam Majeed, Berta Vidal, Chen Wang, Eviatar Yemini, Emily A. Bayer, HaoSheng Sun, Oliver Hobert, David M. Miller III, Marc Hammarlund
bioRxiv 2022.04.05.487209; doi: https://doi.org/10.1101/2022.04.05.487209

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