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Series GSE52136 Query DataSets for GSE52136
Status Public on Apr 10, 2014
Title Effect of Aid deletion on the global DNA methylation status of iPS cells
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary It has been shown that DNA demethylation has a pivotal role in the generation of induced pluripotent stem (iPS) cells. However, the underlying mechanism is still unclear. Previous reports indicated that activation-induced cytidine deaminase (Aid) is involved in DNA demethylation in several developmental processes and cell fusion-mediated reprogramming. Based on the reports, we hypothesized that Aid may be involved in DNA demethylation during the iPS cell generation. In this study, we examined the function of Aid in iPS cell generation using Aid knockout (Aid-/-) mice expressing a GFP reporter under the control of a pluripotent stem cell marker, Nanog. By the introduction of Oct3/4, Sox2, Klf4 and c-Myc, Nanog-GFP positive iPS cells could be generated from the fibroblasts and primary B cells of Aid-/- mice. The Aid-/- iPS cells showed normal proliferation and gave rise to chimeras, indicating their capacity for self-renewal and pluripotency. The comprehensive DNA methylation analysis by MBD-sequening demonstrated that there were only a few differences between Aid+/+ and Aid-/- iPS cells.
Overall design Aid+/+ and Aid-/- iPS colonies were generated from Aid+/+ and Aid-/- MEFs and picked up mechanically. The clones were passaged four times on feeder cells and two times on gelatin-coated dishes to exclude the contamination of feeder cells. Subsequently, the genome was isolated. Four Aid+/+ iPS cell clones and four Aid-/- iPS cell clones were compared. To confirm the validity of MBD-sequencing, four Aid+/+ iPS cell clones were compared with three ES cell clones or three Aid+/+ MEFs.
Contributor(s) Shimamoto R
Citation(s) 24718089
Submission date Nov 06, 2013
Last update date May 15, 2019
Contact name Ren Shimamoto
Organization name Center for iPS Cell Research and Application (CiRA)
Department Dept. of Reprogramming Science
Lab Shinya Yamanaka
Street address 53 Shogoin Kawahara-cho, Sakyo-ku
City Kyoto
ZIP/Postal code 606-8507
Country Japan
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (14)
GSM1260176 967B2_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin
GSM1260177 967B4 _Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin
GSM1260178 979B1_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin
BioProject PRJNA227013
SRA SRP032746

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Supplementary file Size Download File type/resource
GSE52136_RAW.tar 19.7 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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