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

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.

SUBMITTER: Overbey EG 

PROVIDER: S-EPMC8044432 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Overbey Eliah G EG   Saravia-Butler Amanda M AM   Zhang Zhe Z   Rathi Komal S KS   Fogle Homer H   da Silveira Willian A WA   Barker Richard J RJ   Bass Joseph J JJ   Beheshti Afshin A   Berrios Daniel C DC   Blaber Elizabeth A EA   Cekanaviciute Egle E   Costa Helio A HA   Davin Laurence B LB   Fisch Kathleen M KM   Gebre Samrawit G SG   Geniza Matthew M   Gilbert Rachel R   Gilroy Simon S   Hardiman Gary G   Herranz Raúl R   Kidane Yared H YH   Kruse Colin P S CPS   Lee Michael D MD   Liefeld Ted T   Lewis Norman G NG   McDonald J Tyson JT   Meller Robert R   Mishra Tejaswini T   Perera Imara Y IY   Ray Shayoni S   Reinsch Sigrid S SS   Rosenthal Sara Brin SB   Strong Michael M   Szewczyk Nathaniel J NJ   Tahimic Candice G T CGT   Taylor Deanne M DM   Vandenbrink Joshua P JP   Villacampa Alicia A   Weging Silvio S   Wolverton Chris C   Wyatt Sarah E SE   Zea Luis L   Costes Sylvain V SV   Galazka Jonathan M JM  

iScience 20210326 4

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 detect  ...[more]

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