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Series GSE141521 Query DataSets for GSE141521
Status Public on Dec 06, 2019
Title Epigenetic signature of human induced pluripotent stem cells identified with the linear machine learning model
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Human induced pluripotent stem cells (iPSCs) were established as an artificial embryonic stem cells (ESCs) to avoid immune rejection, for ethical issues in regenerative medicine, and for biological research. Comparison analyses in previous studies revealed that there is no hot spot that distinguishes iPSCs from ESCs. We herewith established a learning model using Jubatus, as a machine learning platform, with linear model for classification to distinguish human iPSCs from ESCs based on DNA methylation profiles. We found that the linear model classification is most suitable for the analysis of human iPSCs whose line number is practically 10 to 100. The learning models discriminated ESCs and iPSCs with an accuracy of ≥ 85.71 % and ≥ 90.91 %, respectively. In addition, the epigenetic signature of iPSCs was identified by component analysis of the learning models. The iPSC-specific fluctuated methylation regions were abundant at chromosome 7, 8, 12, and 22. The method can be utilized with comprehensive data and can also be widely applied to many aspects of molecular biology research.
 
Overall design Bisulfite converted DNA were hybridised to the Illumina Infinium Human Methylation450K Beadchip or Infunium MethylationEPIC
 
Contributor(s) Nishino K, Takasawa K, Okamura K, Arai Y, Sekiya A, Akutsu H, Umezawa A
Citation(s) 32210272, 33047283
Submission date Dec 05, 2019
Last update date Jan 19, 2021
Contact name Koichiro Nishino
E-mail(s) aknishino@cc.miyazaki-u.ac.jp
Organization name University of Miyazaki
Department Veterinary Medicine
Lab Veterinary Biochemistry and Molecular Biology
Street address 1-1 Gakuen-Kibanadai-Nishi
City Miyazaki
State/province Miyazaki
ZIP/Postal code 889-2192
Country Japan
 
Platforms (2)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL21145 Infinium MethylationEPIC
Samples (18)
GSM4205544 ES-HUES-2_P21
GSM4205545 ES-SEES-03_P30
GSM4205546 ES-SEES-06_P45
Relations
BioProject PRJNA593774

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

Supplementary file Size Download File type/resource
GSE141521_Matrix_signal_intensities_GPL13534.txt.gz 53.5 Mb (ftp)(http) TXT
GSE141521_Matrix_signal_intensities_GPL21145.txt.gz 47.6 Mb (ftp)(http) TXT
GSE141521_RAW.tar 523.5 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table

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