Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Stabilization competency signature

ABSTRACT: Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture required for successful reprogramming mRNA profilling 4 SI clones at 5 time points, 4 SC clones at 6 time points, and 3 feeder samples.

ORGANISM(S): Mus musculus

SUBMITTER: Yu Liu

PROVIDER: E-GEOD-42100 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network.

Golipour Azadeh A David Laurent L Liu Yu Y Jayakumaran Gowtham G Hirsch Calley L CL Trcka Dan D Wrana Jeffrey L JL

Cell stem cell 20121201 6

Reprogramming of somatic cells to a pluripotent state via expression of Oct4, Klf4, Myc, and Sox2 is a multistep process involving phased changes in gene expression. Here, we focus on the later stages of reprogramming, termed maturation and stabilization. We show that the stabilization phase and the acquisition of pluripotency are dependent on the removal of transgene expression late in the maturation phase. Clonal analysis of cells undergoing reprogramming revealed subsets of stabilization-comp ...[more]

PMID: 23217423

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Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

Dataset Information

Stabilization competency signature

Publications

A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network.

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