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Series GSE36290 Query DataSets for GSE36290
Status Public on Dec 06, 2013
Title High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both "tetra-on" and corresponding "tetra-off" iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells.
 
Overall design Examination of the mRNA expression in 13 cell types
 
Contributor(s) Chang G, Gao S, Cai T, Tian J, Gao S
Citation(s) 24381111, 28114969, 26979597
Submission date Mar 06, 2012
Last update date May 29, 2020
Contact name Tao Cai
E-mail(s) caitao@nibs.ac.cn
Organization name National Institute Of Biological Sciences, Beijing (NIBS)
Lab Sequencing Facility
Street address No. 7 Science Park Road, Zhongguancun Life Science Park
City Beijing
ZIP/Postal code 102206
Country China
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (26)
GSM886452 R1-ESC rep1 RNAseq
GSM886453 R1-ESC rep2 RNAseq
GSM886454 1-MEF-iPSC-37 rep1 RNAseq
This SubSeries is part of SuperSeries:
GSE36294 High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells
Relations
SRA SRP011318
BioProject PRJNA155807

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE36290_RAW.tar 27.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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