E-GEOD-59569 - The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors

Status
Released on 30 July 2014, last updated on 6 September 2014
Organism
Mus musculus
Samples (19)
Protocols (3)
Description
Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4 and Myc (OSKM) into somatic cells. Though iPSCs are pluripotent, they frequently exhibit high variation in their quality as measured by chimera contribution and tetraploid (4n) complementation. Thus, improving the quality of iPSCs is an indispensable prerequisite for future iPSC-based therapy. Here we show that one major determinant for iPSCs quality is the combination of reprograming factor selected. Ectopic expression of Sall4, Nanog, Esrrb and Lin28 (SNEL) in MEFs efficiently generated high quality iPSCs as compared to other combinations of factors. SNEL-iPSCs produced approximately 5 times more efficiently “all-iPSC” mice compared to OSKM-iPSCs. While differentially methylated regions, transcript number of master regulators, establishment of ESC-specific super enhancers, and global aneuploidy were comparable between the lines, aberrant expression of 1,765 genes, trisomy of chromosome 8 and abnormal H2A.X deposition were frequently observed in poor quality OSK-iPSCs and OSKM-iPSCs. ChIP-Seq for Med1 in reprogrammed and partially reprogrammed mouse embryonic stem cell lines and corresponding controls
Experiment type
ChIP-seq 
Contacts
Richard A Young <young_computation@wi.mit.edu>, Andrew Xiao, Batool Akhtar-Zaidi, Brian J Abraham, David Porubsky, Dina Faddah, Elisabeth Kulenkampff, Heather Hoke, Johanna Goldmann, Joseph R Ecker, Joseph R Nery, Kibibi Ganz, Linyu Shi, Malkiel Cohen, Matthew D Schultz, Niek van Wiemartschen, Peter M Lansdorp, Qing Gao, Rudolf Jaenisch, Sovan Sarkar, Styliana Markoulaki, Tao Wu, Yosef Buganim, Yupeng He
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-59569.idf.txt
Sample and data relationshipE-GEOD-59569.sdrf.txt
Processed data (14)Click to browse processed data
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