Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Abstract RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (Illumina sequencing by synthesis and MGI DNBSEQ™) and two microarray platforms (Illumina Expression BeadChip and GeneChip™ Human Transcriptome Array 2.0) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA sequencing combined with DNB-seq produced a multitude of genes of biological relevance and significance in response to recombinant human erythropoietin, in contrast to other platforms. Through data triangulation linking genes to functions, genes representing the processes of erythropoiesis as well as non-erythropoietic functions of erythropoietin were unveiled. This study provides a knowledge base of genes characterising the responses to recombinant human erythropoietin through cross-platform comparison and validation.

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Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Scientific Reports ◽

10.1038/s41598-021-00608-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Guan Wang ◽

Traci Kitaoka ◽

Ali Crawford ◽

Qian Mao ◽

Andrew Hesketh ◽

...

Keyword(s):

Recombinant Human Erythropoietin ◽

Target Genes ◽

Rna Seq ◽

Pathway Enrichment ◽

Human Erythropoietin ◽

Tissue Protection ◽

Wide Range ◽

Rna Biology ◽

Cross Platform ◽

Differential Gene

AbstractRNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2.0 and Illumina Expression BeadChip) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA DNB-seq generated a multitude of target genes compared to other platforms. Pathway enrichment analyses revealed genes correlate to not only erythropoiesis and oxygen transport but also a wide range of other functions, such as tissue protection and immune regulation. This study provides a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.

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Faculty Opinions recommendation of Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717971189.793469500 ◽

2013 ◽

Author(s):

Stephen Turner

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Rna Seq ◽

Web Tool ◽

Differential Gene

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Differential Gene Expression by RNA-Seq Analysis of the Primo Vessel in the Rabbit Lymph

Journal of Acupuncture and Meridian Studies ◽

10.1016/j.jams.2018.10.008 ◽

2019 ◽

Vol 12 (1) ◽

pp. 11-19 ◽

Cited By ~ 1

Author(s):

Jun-Young Shin ◽

Sang-Heon Choi ◽

Da-Woon Choi ◽

Ye-Jin An ◽

Jae-Hyuk Seo ◽

...

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Rna Seq ◽

Differential Gene

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A Unified Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2018.2790918 ◽

2019 ◽

Vol 16 (2) ◽

pp. 442-454 ◽

Cited By ~ 5

Author(s):

Kefei Liu ◽

Jieping Ye ◽

Yang Yang ◽

Li Shen ◽

Hui Jiang

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Unified Model ◽

Rna Seq ◽

Differential Gene

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RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

Genes ◽

10.3390/genes11121487 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1487

Author(s):

Marie Lataretu ◽

Martin Hölzer

Keyword(s):

Gene Expression ◽

Homo Sapiens ◽

Standard Technique ◽

Common Species ◽

Rna Seq ◽

Rna Molecules ◽

Gene Filtering ◽

Differential Gene ◽

High Level ◽

Very High

RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.

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