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| 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.
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| 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.
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| Contributor(s) |
Shimamoto R |
| Citation(s) |
24718089 |
| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ren Shimamoto |
| E-mail(s) |
shimamoto@cira.kyoto-u.ac.jp
|
| 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
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| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (14)
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| 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 |
| GSM1260179 |
979B3_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin |
| GSM1260180 |
979F1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin |
| GSM1260181 |
979F3_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin |
| GSM1260182 |
981E1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin |
| GSM1260183 |
981E4_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin |
| GSM1260184 |
RF8_ES cells_p19_cultured on gelatin |
| GSM1260185 |
MG1.19_ES cells_cultured on gelatin |
| GSM1260186 |
B6 ES_ES cells_cultured on gelatin |
| GSM1260187 |
Aid+/+ MEF#1_p3 |
| GSM1260188 |
Aid+/+ MEF#2_p3 |
| GSM1260189 |
Aid+/+ MEF#3_p3 |
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| Relations |
| BioProject |
PRJNA227013 |
| SRA |
SRP032746 |
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