Identification of the new gene Zrsr1 to associate with the pluripotency state in induced pluripotent stem cells (iPSCs) using high throughput sequencing technology

Shuai Gao; Gang Chang; Jianhui Tian; Shaorong Gao; Tao Cai

doi:10.1016/j.gdata.2014.04.008

Identification of the new gene Zrsr1 to associate with the pluripotency state in induced pluripotent stem cells (iPSCs) using high throughput sequencing technology

Genom Data. 2014 Apr 30:2:73-7. doi: 10.1016/j.gdata.2014.04.008. eCollection 2014 Dec.

Authors

Shuai Gao¹, Gang Chang¹, Jianhui Tian², Shaorong Gao³, Tao Cai³

Affiliations

¹ Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction; National Engineering Laboratory for Animal Breeding; College of Animal Sciences and Technology, China Agricultural University, Beijing 100193, China ; National Institute of Biological Sciences, NIBS, Beijing 102206, China.
² Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction; National Engineering Laboratory for Animal Breeding; College of Animal Sciences and Technology, China Agricultural University, Beijing 100193, China.
³ National Institute of Biological Sciences, NIBS, Beijing 102206, China.

Abstract

Finding the markers to predict the quality of induced pluripotent stem cells (iPSCs) will accelerate its practical application. The fully pluripotent iPSCs has been determined as viable all-iPSC mice can be generated through tetraploid (4N) complementation. The activation of the imprinted Dlk1-Dio3 gene cluster was reported to correlate with the pluripotency of iPSCs. However, recent studies demonstrated that the loss of imprinting at the Dlk1-Dio3 locus does not strictly correlate with the reduced pluripotency of iPSCs. In our study (ref [1]), iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was well characterized using tetraploid (4N) complementation assay. The gene expression and global epigenetic modifications of "4N-ON" and the corresponding "4N-OFF" iPSC lines were compared through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4me3, H3K27me3 and H3K4me2) and DNA methylation. Very few differences were detected in the iPSC lines that were investigated. However, an imprinted gene, Zrsr1 was disrupted in the "4N-OFF" iPSC lines. Here we provide more detail about the dataset and the R script with additional data for others to repeat the finding.