Unknown,Transcriptomics,Genomics,Proteomics

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Blimp1 expression predicts embryonic stem cell development in vitro

ABSTRACT: Comparing global transcriptional profile between standard or 2i derived ES cell lines. RNA extracted from established ES cell lines either from standard derivation condition or 2i derivation condition, all cultured without 2i after derivation.

ORGANISM(S): Mus musculus

SUBMITTER: Thomas Zwaka

PROVIDER: E-GEOD-31868 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Blimp1 expression predicts embryonic stem cell development in vitro.

Chu Li-Fang LF Surani M Azim MA Jaenisch Rudolf R Zwaka Thomas P TP

Current biology : CB 20111013 20

Despite recent critical insights into the pluripotent state of embryonic stem cells (ESCs), there is little agreement over the inaugural and subsequent steps leading to its generation [1-4]. Here we show that inner cell mass (ICM)-generated cells expressing Blimp1, a key transcriptional repressor of the somatic program during germ cell specification [5, 6], emerge on day 2 of blastocyst culture. Single-cell gene expression profiling indicated that many of these Blimp1-positive cells coexpress ot ...[more]

PMID: 22000107

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Project description:Hepatocytes that have differentiated from human embryonic stem cells have great potential for the treatment of liver disease as well as for drug testing. Moreover, in vitro hepatogenesis is a powerful model system for studying the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism that influences differential gene expression during embryonic development. We profiled gene expression and DNA methylation of three cell states of in vitro hepatogenesis—human embryonic stem cells, endoderm progenitors, and mature hepatocytes—using microarray analysis. Among 525 state-specific expressed genes, 67 showed significant negative correlation between gene expression and DNA methylation. State-specific expression and methylation of target genes were validated by quantitative reverse transcription–PCR and pyrosequencing, respectively. To elucidate genome-scale methylation changes beyond the promoter, we also performed high-throughput sequencing of methylated DNA captured by MBD2 protein [see SRA link below]. We found dynamic methylation changes in intergenic regions of the human genome during differentiation. Conclusion: This study provides valuable methylation markers for the lineage commitment of in vitro hepatogenesis and should help elucidate the molecular mechanisms underlying stem cell differentiation and liver development. ES, EP, and MH methylation assays were run in triplicate. Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research, Orange, CA), and 200 ng of the converted DNA was used for amplification. Amplified DNA was hybridized to the Infinium HumanMethylation27 BeadChip (Illumina), which analyzes the methylation status of 27,578 CpG sites selected from more than 14,495 well-annotated genes. The arrays were imaged using the BeadArray Reader, and image processing and extraction of intensity data were performed according to Illumina’s instructions. Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines).

Dataset Information

Blimp1 expression predicts embryonic stem cell development in vitro

Publications

Blimp1 expression predicts embryonic stem cell development in vitro.

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