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

Guan Wang; Traci Kitaoka; Ali Crawford; Qian Mao; Andrew Hesketh; Fergus Guppy; Garrett I. Ash; Jason  Liu; Mark  Gerstein; Yannis Pitsiladis

doi:10.1038/s41598-021-00608-9

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

Guan Wang
, Traci Kitaoka
, Ali Crawford
, Qian Mao
, Andrew Hesketh
, Fergus Guppy
, Garrett I. Ash
, Jason Liu
, Mark Gerstein
, Yannis Pitsiladis

Research output: Contribution to journal › Article › peer-review

Abstract

RNA-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.

Original language	English
Article number	21705
Journal	Scientific Reports
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41598-021-00608-9
Publication status	Published - 4 Nov 2021

Bibliographical note

Funding Information:
We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.

Keywords

MGI DNB-seq
Illumina mRNA-seq
GeneChip Human Transcriptome Array 2.0
Illumina Expression BeadChip
Recombinant human erythropoietin
Differential gene expression
Biological pathways

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Cite this

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title = "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 (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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author = "Guan Wang and Traci Kitaoka and Ali Crawford and Qian Mao and Andrew Hesketh and Fergus Guppy and Ash, \{Garrett I.\} and Jason Liu and Mark Gerstein and Yannis Pitsiladis",

note = "Funding Information: We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.",

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doi = "10.1038/s41598-021-00608-9",

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AU - Wang, Guan

AU - Kitaoka, Traci

AU - Crawford, Ali

AU - Mao, Qian

AU - Hesketh, Andrew

AU - Guppy, Fergus

AU - Ash, Garrett I.

AU - Liu, Jason

AU - Gerstein, Mark

AU - Pitsiladis, Yannis

N1 - Funding Information: We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.

PY - 2021/11/4

Y1 - 2021/11/4

N2 - RNA-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.

AB - RNA-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.

KW - MGI DNB-seq

KW - Illumina mRNA-seq

KW - GeneChip Human Transcriptome Array 2.0

KW - Illumina Expression BeadChip

KW - Recombinant human erythropoietin

KW - Differential gene expression

KW - Biological pathways

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DO - 10.1038/s41598-021-00608-9

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SN - 2045-2322

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JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 21705

ER -

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

Abstract

Bibliographical note

Keywords

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