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Series GSE74967 Query DataSets for GSE74967
Status Public on Jul 27, 2016
Title Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins.
Overall design Methyl-seq analysis for undifferentiated induced pluripotent stem cell (iPSC) lines (n = 21), human dermal fibroblast (HDF, n = 1), human peripheral blood (n = 1), and human keratinocyte (n = 1), and ATAC-seq analysis for 2 iPSC lines and an embryonic stem cell (ESC) line with two different culture conditions. CTCF-ChIP-seq analysis for an ESC line.
Contributor(s) Nishizawa M, Nakamura M, Watanabe A, Yoshida Y
Citation(s) 27476965
Submission date Nov 12, 2015
Last update date May 15, 2019
Contact name Akira Watanabe
Organization name CyberomiX Inc
Street address Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 602-8407
Country Japan
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (29)
GSM1939248 585A1
GSM1939249 585B1
GSM1939250 648B1
BioProject PRJNA302057
SRA SRP066123

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Supplementary file Size Download File type/resource
GSE74967_RAW.tar 1.5 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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