Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

Jani de Vos; Richard P.M.A. Crooijmans; Martijn F.L. Derks; Susan L. Kloet; Bert Dibbits; Martien A.M. Groenen; Ole Madsen

doi:10.1016/j.isci.2023.106252

Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

Jani de Vos^*, Richard P.M.A. Crooijmans, Martijn F.L. Derks, Susan L. Kloet, Bert Dibbits, Martien A.M. Groenen, Ole Madsen

^*Corresponding author for this work

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

1 Citation (Scopus)

Abstract

The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.

Original language	English
Article number	106252
Journal	iScience
Volume	26
Issue number	3
DOIs	https://doi.org/10.1016/j.isci.2023.106252
Publication status	Published - 17 Mar 2023

Keywords

Cell biology

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10.1016/j.isci.2023.106252Licence: CC BY

https://edepot.wur.nl/590639Licence: CC BY

FAANG Chicken SL-29 cell line
de Vos, J. (Creator), Crooijmans, R. P. M. A. (Creator), Derks, M. F. L. (Creator), Kloet, S. L. (Creator), Dibbits, B. (Creator), Groenen, M. A. M. (Creator) & Madsen, O. (Creator), Wageningen University & Research, 28 Feb 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB59475
Dataset
FAANG Pig IPECJ2 cell line
de Vos, J. (Creator), Crooijmans, R. P. M. A. (Creator), Derks, M. F. L. (Creator), Kloet, S. L. (Creator), Dibbits, B. (Creator), Groenen, M. A. M. (Creator) & Madsen, O. (Creator), Wageningen University & Research, 28 Feb 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB59474
Dataset

Cite this

@article{7c91a157495b4774a50cc2b30787aa0e,

title = "Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines",

abstract = "The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.",

keywords = "Cell biology",

author = "{de Vos}, Jani and Crooijmans, {Richard P.M.A.} and Derks, {Martijn F.L.} and Kloet, {Susan L.} and Bert Dibbits and Groenen, {Martien A.M.} and Ole Madsen",

year = "2023",

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doi = "10.1016/j.isci.2023.106252",

language = "English",

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T1 - Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

AU - de Vos, Jani

AU - Crooijmans, Richard P.M.A.

AU - Derks, Martijn F.L.

AU - Kloet, Susan L.

AU - Dibbits, Bert

AU - Groenen, Martien A.M.

AU - Madsen, Ole

PY - 2023/3/17

Y1 - 2023/3/17

N2 - The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.

AB - The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.

KW - Cell biology

U2 - 10.1016/j.isci.2023.106252

DO - 10.1016/j.isci.2023.106252

M3 - Article

AN - SCOPUS:85149663537

SN - 2589-0042

VL - 26

JO - iScience

JF - iScience

IS - 3

M1 - 106252

ER -

Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

Abstract

Keywords

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Datasets

FAANG Chicken SL-29 cell line

FAANG Pig IPECJ2 cell line

Cite this