文章基本信息

标题：NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
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作者：Eliah G. Overbey ; Amanda M. Saravia-Butler ; Zhe Zhang 等
期刊名称：iScience
印刷版ISSN：2589-0042
出版年度：2021
卷号：24
期号：4
页码：1-22
DOI：10.1016/j.isci.2021.102361
语种：English
出版社：Elsevier
摘要：SummaryWith 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.Graphical abstractDisplay OmittedHighlights•Analysis of omics data from different spaceflight studies presents unique challenges•A standardized pipeline for RNA-seq analysis eliminates data processing variation•The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE•Space-relevant data processed with this pipeline are available at genelab.nasa.govOmics; Space Sciences