Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons [preprint]
Authors
Barrett, AlecVarol, Erdem
Weinreb, Alexis
Taylor, Seth R.
McWhirter, Rebecca M.
Cros, Cyril
Basaravaju, Manasa
Poff, Abigail
Tipps, John A.
Majeed, Maryam
Vidal, Berta
Wang, Chen
Yemini, Eviatar
Bayer, Emily A.
Sun, HaoSheng
Hobert, Oliver
Miller, David M.
Hammarlund, Marc
Document Type
PreprintPublication Date
2022-04-08
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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.Source
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/10.1101/2022.04.05.487209DOI
10.1101/2022.04.05.487209Permanent Link to this Item
http://hdl.handle.net/20.500.14038/51552Notes
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.Rights
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.; Attribution-NonCommercial-NoDerivatives 4.0 InternationalDistribution License
http://creativecommons.org/licenses/by-nc-nd/4.0/ae974a485f413a2113503eed53cd6c53
10.1101/2022.04.05.487209
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Except where otherwise noted, this item's license is described as 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.