Concordance of Affymetrix GeneChip® Human Transcriptome Array 2.0 and USB® VeriQuest™ real‐time PCR data (LB207)

Újvári, Andrea; Chamnongpol, Sangpen; Kourennaia, Olga; Myers, Kim; Bressler, Vincent; Hubbard, J. C.; Schweitzer, Anthony; Kubu, Chris J.

doi:10.1096/fasebj.28.1_supplement.lb207

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“…The microarray, a recent development of Affymetrix, is not only able to screen 44,699 transcript clusters but additionally has 339,146 probes against splicing junctions, which allows for the specific detection of splicing sites. Therefore, it is a highly standardized, mature representative of microarray development [42]. The RNA-Seq data set was generated in a standard approach with a sequencing depth of 25 million and 75 bp paired-end reads.…”

Section: Resultsmentioning

confidence: 99%

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data

Vahlensieck

Thiel

Adelmann

et al. 2021

IJMS

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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.

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Section: Resultsmentioning

confidence: 99%