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NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data

Overbey, Eliah G.; G Overbey, Eliah; Saravia-Butler, Amanda M.; M Saravia-Butler, Amanda; Zhang, Zhe; Rathi, Komal S.; S Rathi, Komal; Fogle, Homer; Abraham da Silveira, Willian; Barker, Richard J.; J Barker, Richard; Bass, Joseph J.; J Bass, Joseph; Beheshti, Afshin; Berrios, Daniel C.; C Berrios, Daniel; Blaber, Elizabeth A.; A Blaber, Elizabeth; Cekanaviciute, Egle; Costa, Helio A.; A Costa, Helio; Davin, Laurence B.; B Davin, Laurence; Fisch, Kathleen M.; M Fisch, Kathleen; Gebre, Samrawit G.; G Gebre, Samrawit; Geniza, Matthew; Gilbert, Rachel; Gilroy, Simon; Hardiman, Gary; Herranz, Raúl; Kidane, Yared H.; H Kidane, Yared; Kruse, Colin P.S.; P S Kruse, Colin; Lee, Michael D.; D Lee, Michael; Liefeld, Ted; Lewis, Norman G.; G Lewis, Norman; McDonald, J. Tyson; Tyson McDonald, J; Meller, Robert; Mishra, Tejaswini; Perera, Imara Y.; Y Perera, Imara; Ray, Shayoni; Reinsch, Sigrid S.; S Reinsch, Sigrid; Rosenthal, Sara; Brin Rosenthal, Sara; Strong, Michael; Szewczyk, Nathaniel J.; J...

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Authors

Eliah G. Overbey

Eliah G Overbey

Amanda M. Saravia-Butler

Amanda M Saravia-Butler

Zhe Zhang

Komal S. Rathi

Komal S Rathi

Homer Fogle

Richard J. Barker

Richard J Barker

Joseph J. Bass

Joseph J Bass

Afshin Beheshti

Daniel C. Berrios

Daniel C Berrios

Elizabeth A. Blaber

Elizabeth A Blaber

Egle Cekanaviciute

Helio A. Costa

Helio A Costa

Laurence B. Davin

Laurence B Davin

Kathleen M. Fisch

Kathleen M Fisch

Samrawit G. Gebre

Samrawit G Gebre

Matthew Geniza

Rachel Gilbert

Simon Gilroy

Gary Hardiman

Raúl Herranz

Yared H. Kidane

Yared H Kidane

Colin P.S. Kruse

Colin P S Kruse

Michael D. Lee

Michael D Lee

Ted Liefeld

Norman G. Lewis

Norman G Lewis

J. Tyson McDonald

J Tyson McDonald

Robert Meller

Tejaswini Mishra

Imara Y. Perera

Imara Y Perera

Shayoni Ray

Sigrid S. Reinsch

Sigrid S Reinsch

Sara Rosenthal

Sara Brin Rosenthal

Michael Strong

Nathaniel J. Szewczyk

Nathaniel J Szewczyk

Candice G.T. Tahimic

Candice G T Tahimic

Deanne M. Taylor

Deanne M Taylor

Joshua P. Vandenbrink

Joshua P Vandenbrink

Alicia Villacampa

Silvio Weging

Chris Wolverton

Sarah E. Wyatt

Sarah E Wyatt

Luis Zea

Sylvain V. Costes

Sylvain V Costes

Jonathan M. Galazka

Jonathan M Galazka



Abstract

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

Citation

Overbey, E. G., G Overbey, E., Saravia-Butler, A. M., M Saravia-Butler, A., Zhang, Z., Rathi, K. S., …M Galazka, J. (2021). NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data. iScience, 24(4), Article 102361. https://doi.org/10.1016/j.isci.2021.102361

Journal Article Type Article
Acceptance Date Apr 1, 2021
Publication Date Apr 23, 2021
Deposit Date Oct 25, 2024
Publicly Available Date Oct 25, 2024
Journal iScience
Print ISSN 2589-0042
Publisher Cell Press
Peer Reviewed Peer Reviewed
Volume 24
Issue 4
Article Number 102361
DOI https://doi.org/10.1016/j.isci.2021.102361
PMID 33870146

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