NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data.
Omics
Space Sciences
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
23 Apr 2021
23 Apr 2021
Historique:
received:
08
09
2020
revised:
30
10
2020
accepted:
23
03
2021
entrez:
19
4
2021
pubmed:
20
4
2021
medline:
20
4
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33870146
doi: 10.1016/j.isci.2021.102361
pii: S2589-0042(21)00329-1
pmc: PMC8044432
doi:
Types de publication
Journal Article
Langues
eng
Pagination
102361Subventions
Organisme : NCI NIH HHS
ID : R50 CA243876
Pays : United States
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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