Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data
| العنوان: | Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data |
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| المؤلفون: | Jennifer Polzer, Cora S. Thiel, Beatrice A. Lauber, Oliver Ullrich, Jan Adelmann, Christian Vahlensieck |
| المساهمون: | University of Zurich, Thiel, Cora S, Ullrich, Oliver |
| المصدر: | International Journal of Molecular Sciences, Vol 22, Iss 8451, p 8451 (2021) International Journal of Molecular Sciences Volume 22 Issue 16 |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Transcriptional Activation, Jurkat T cells, Microarray, 10017 Institute of Anatomy, QH301-705.5, 1503 Catalysis, T-Lymphocytes, 1607 Spectroscopy, RNA-Seq, 610 Medicine & health, Computational biology, Biology, Jurkat cells, Article, Catalysis, Inorganic Chemistry, Transcriptome, spaceflight, transcriptomics, Jurkat Cells, Gene expression, 1312 Molecular Biology, 1706 Computer Science Applications, Humans, Physical and Theoretical Chemistry, Biology (General), Molecular Biology, Gene, QD1-999, Spectroscopy, hypergravity, Hypergravity, Microarray analysis techniques, 1604 Inorganic Chemistry, Organic Chemistry, General Medicine, Space Flight, microgravity, Computer Science Applications, ground-based facilities, Chemistry, 10076 Center for Integrative Human Physiology, 570 Life sciences, biology, 1606 Physical and Theoretical Chemistry, microarray, altered gravity, 1605 Organic Chemistry |
| الوصف: | Cellular responses to micro- and hypergravity are rapid and complex and appear within the first few seconds of exposure. Transcriptomic analyses are a valuable tool to analyze these genome-wide cellular alterations. For a better understanding of the cellular dynamics upon altered gravity exposure, it is important to compare different time points. However, since most of the experiments are designed as endpoint measurements, the combination of cross-experiment meta-studies is inevitable. Microarray and RNA-Seq analyses are two of the main methods to study transcriptomics. In the field of altered gravity research, both methods are frequently used. However, the generation of these data sets is difficult and time-consuming and therefore the number of available data sets in this research field is limited. In this study, we investigated the comparability of microarray and RNA-Seq data and applied the results to a comparison of the transcriptomics dynamics between the hypergravity conditions during two real flight platforms and a centrifuge experiment to identify temporal adaptation processes. We performed a comparative study on an Affymetrix HTA2.0 microarray and a paired-end RNA-Seq data set originating from the same Jurkat T cell RNA samples from a short-term hypergravity experiment. The overall agreeability was high, with better sensitivity of the RNA-Seq analysis. The microarray data set showed weaknesses on the level of single upregulated genes, likely due to its normalization approach. On an aggregated level of biotypes, chromosomal distribution, and gene sets, both technologies performed equally well. The microarray showed better performance on the detection of altered gravity-related splicing events. We found that all initially altered transcripts fully adapted after 15 min to hypergravity and concluded that the altered gene expression response to hypergravity is transient and fully reversible. Based on the combined multiple-platform meta-analysis, we could demonstrate rapid transcriptional adaptation to hypergravity, the differential expression of the ATPase subunits ATP6V1A and ATP6V1D, and the cluster of differentiation (CD) molecules CD1E, CD2AP, CD46, CD47, CD53, CD69, CD96, CD164, and CD226 in hypergravity. We could experimentally demonstrate that it is possible to develop methodological evidence for the meta-analysis of individual data. |
| وصف الملف: | ijms-22-08451-v2.pdf - application/pdf; application/pdf |
| اللغة: | English |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ec05e613dad6787fe988ce0ffa224bf8 https://www.zora.uzh.ch/id/eprint/208849/ |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....ec05e613dad6787fe988ce0ffa224bf8 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |