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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2018 |
| Title |
A Direct and Accelerated Platform for Analyzing Reprogramming by Defined factors |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Somatic cells can be reverted back to a pluripotent state by nuclear transfer, cell fusion, and defined factors, representing three distinct approaches to reprogram cell fate. Unlike cell fusion, reprogramming by nuclear transfer or defined factors gives rise to cells that contribute to the development of a live animal in mouse, thus making a quasi-direct comparison possible Combining optimized culture conditions and modified reprogramming factors, we report here that mouse fibroblasts can be reprogrammed by defined factors into cells capable of contributing to chimera formation and germline transmission in as short as 96 hours, comparable to the time required for the formation of inner cell mass in cloned embryos by nuclear transfer. Gene expression profiling analysis shows that this accelerated reprogramming process in fact corresponds well with previously reported longer ones with similar molecular signatures. Additionally we find a new set of genes activated as the reprogramming cells acquire chimera competency. In a broader sense, this platform may be adopted for applications such as high throughput screenings for reprogramming mediators both chemical and biological, as well as omics-related mechanistic investigations.
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| Overall design |
We examined transcriptome transition during somatic cells reprogramming using two reprogramming systems, OSK system and OvSvK system (Ov is Oct4-vp16 and Sv is Sox2-vp16). We can get reprogrammed cells capable of contributing to chimera formation and germline transmission in 4 day using OvSvK system and 7 day in OSK system, so, we got samples at D0, D1, D2, D3, D4 after OvSvK transfection and performed RNA-seq, similarly, we sequenced the samples at D0, D1, D3, D5, D7 in OSK system. Furthermore, we also sequenced several control samples, such as GFP samples at different time points of reprogramming. At the same time, we examined the effect of several elements on transcriptome during reprogramming, including Vitamin C, bGFG, GSK3 inhibitor(CHIR-99021 and LiCl).
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| Contributor(s) |
Pei D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihui Lin |
| E-mail(s) |
lin_lihui@gibh.ac.cn
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| Phone |
020-32015291
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| Organization name |
Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science
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| Department |
Stem cell
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| Lab |
Pei Duanqing
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| Street address |
No.190, Kaiyuan Street
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
GD20 |
| Country |
China |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA246683 |
| SRA |
SRP041872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57546_RAW.tar |
12.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE57546_all_samples_genes_cpm_expression.tsv.gz |
1017.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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