Transcriptomics

Dataset Information

3

MiRNA Expression In Maintenance and Differentiation of Human Embryonic Stem Cells


ABSTRACT: Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications. To gain better insight into these cells, a clearer understanding of their molecular properties is crucial. In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines. By examining both undifferentiated hESCs and cells exposed to an undirected differentiation scheme at early stages, we found those miRNAs and mRNAs enriched in the hESC lines, and those miRNAs and mRNAs initially regulated upon commitment. In comparing these profiles with those of an embryonal carcinoma (EC) cell line, NTera-2, we observed distinct patterns of miRNA expression in hESCs. Furthermore, we identify several new hESC-enriched miRNAs that respond rapidly to differentiation cues, in addition to miRNAs from a large cluster of hESC-enriched miRNAs located on chromosome 19, and miRNAs from the miR-302 cluster and the miR-17~92 family of clusters. We show that key miRNAs in the chromosome 19 cluster are highly enriched in hESCs in comparison to NTera-2, and might therefore serve as future diagnostic markers for stem cell capacity. Examination of changes in mRNA expression during early commitment further reveals that many differentiation-regulated genes are possible candidates for regulation by these hESC-enriched miRNAs. A set of 9 different NIH-approved hESC lines were treated with conditions to promote either maintenance of an undifferentiated state (mouse embryonic fibroblast- conditioned media) or undirected differentiation of the hESCs into various cell lineages (DMEM + 20% FBS). RNA was harvested from the cells and subjected to miRNA microarray analysis. An embryonal carcinma cell line, NTera-2, which shows similar growth characteristics to hESCs was used an additional comparative sample. Additionally, human placental RNA samples were used as internal controls for miRNA microarray slide (Agilent Technologies). The miRNA expression data was used to analyze differential miRNA expression in each specific cell line, as well as large-scale comparisons of the undifferentiated and differentiated hESC lines.

ORGANISM(S): Homo sapiens  

SUBMITTER: Garrick Peters   Bradford M Stadler  Irena Ivanovska  Michele Cleary  Sunny Song  Hannele Ruohola-Baker  Christopher Darby  C A Blau  Carol Ware  Angelique Nelson  Kshama Mehta  Bradford Stadler 

PROVIDER: E-GEOD-14473 | ArrayExpress | 2010-09-09

SECONDARY ACCESSION(S): GSE14473PRJNA111477

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

2009-09-01 | GSE14473 | GEO
2010-05-07 | GSE21722 | GEO
2010-05-06 | E-GEOD-21722 | ArrayExpress
| GSE59380 | GEO
2015-02-01 | E-GEOD-62501 | ArrayExpress
2018-05-16 | PXD007271 | Pride
2018-05-16 | PXD007738 | Pride
2018-05-16 | PXD007270 | Pride
2013-12-03 | E-GEOD-42446 | ArrayExpress
2014-01-18 | E-GEOD-54186 | ArrayExpress