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

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › peer-review

8 Citations (Scopus)

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

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SDG 3 Good Health and Well-being

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10.1038/s41598-021-00608-9

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.",

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: Tis 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 Ofce of Academic Afliations at the United States Veterans Health Administration. Publisher Copyright: {\textcopyright} The Author(s) 2021",

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

language = "English",

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TY - JOUR

T1 - Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

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: Tis 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 Ofce of Academic Afliations at the United States Veterans Health Administration. Publisher Copyright: © The Author(s) 2021

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.

UR - https://www.scopus.com/pages/publications/85118650041

U2 - 10.1038/s41598-021-00608-9

DO - 10.1038/s41598-021-00608-9

M3 - Journal article

SN - 2045-2322

VL - 11

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 21705

ER -

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

Abstract

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