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Expression profiles of miRNA derived from cells for ectoderm-biased substate of human pluripotent stem cells.

ABSTRACT: Expression profiles of miRNA derived from cells for ectoderm-biased substate of human pluripotent stem cells.

PROVIDER: PRJNA508803 | ENA |

REPOSITORIES: ENA

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mRNA expression profiles for ectoderm-biased substate of human pluripotent stem cells.

Project description:mRNA expression profiles for ectoderm-biased substate of human pluripotent stem cells.

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Expression profiles of miRNA derived from exosomes for ectoderm-biased substate of human pluripotent stem cells.

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mRNA and miRNA expression profiles in an ectoderm-biased substate of human pluripotent stem cells.

Project description:The potential applications of human pluripotent stem cells, embryonic stem (ES) cells, and induced pluripotent stem (iPS) cells in cell therapy and regenerative medicine have been widely studied. The precise definition of pluripotent stem cell status during culture using biomarkers is essential for basic research and regenerative medicine. Culture conditions, including extracellular matrices, influence the balance between self-renewal and differentiation. Accordingly, to explore biomarkers for defining and monitoring the pluripotent substates during culture, we established different substates in H9 human ES cells by changing the extracellular matrix from vitronectin to Matrigel. The substate was characterised by low and high expression of the pluripotency marker R-10G epitope and the mesenchymal marker vimentin, respectively. Immunohistochemistry, induction of the three germ layers, and exhaustive expression analysis showed that the substate was ectoderm-biased, tended to differentiate into nerves, but retained the potential to differentiate into the three germ layers. Further integrated analyses of mRNA and miRNA microarrays and qPCR analysis showed that nine genes (COL9A2, DGKI, GBX2, KIF26B, MARCH1, PLXNA4, SLC24A4, TLR4, and ZHX3) were upregulated in the ectoderm-biased cells as ectoderm-biased biomarker candidates in pluripotent stem cells. Our findings provide important insights into ectoderm-biased substates of human pluripotent stem cells in the fields of basic research and regenerative medicine.

| S-EPMC6695399 | biostudies-literature

RNA-seq profiles of pluripotent and surface ectoderm cells with and without p63

Project description:Purpose: Evaluate p63 regulation of gene expression in human embryonic stem cells and the surface ectoderm Methods: RNA profiles for human embyronic stem cells and surface ectoderm cells with and without p63 using deep sequencing, in duplicate, on Illumina NextSeq 500 sequencer. Quality of reads were checked by fastqc. Reads were aligned to hg19 genome using tophat and FPKM values were generated using Homer. Results: p63 is largely unable to regulate gene expression in pluripotent cells, but acts primarily as a repressor in the surface ectoderm. Conclusion: p63 regulation of gene expression is dependent on the changes the cell undergoes during surface ectoderm commitment

2018-11-06 | GSE121994 | GEO

RNA-seq profiles of pluripotent and surface ectoderm cells with and without p63

Project description:RNA-seq profiles of pluripotent and surface ectoderm cells with and without p63

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Genome-wide chromatin accessibility in pluripotent and surface ectoderm cells with and without p63

Project description:Purpose: Evaluate changes in chromatin accessibility between human embryonic stem cells and surface ectoderm cells with and without the transcription factor p63. Method: Chromatin accessibility profiles for human embryonic stem cells and surface ectoderm with and without p63 were generated by deep sequencing, in duplicate, with the Illumina NextSeq sequencer. Quality reads were assessed by fastq. Reads were aligned using Bowtie2, PCR duplicates and mitochondrial DNA were discarded, and peak calling was completed using MACS2. Non-reproducible peaks were filtered out by IDR with an FDR of 5%. Results: p63 fails to modify chromatin accessibility when ectopically expressed in human embryonic stem cells; differentiation of human embryonic stem cells to surface ectoderm results in the closure of some regions open in pluripotent cells and the opening of new regions; and loss of p63 in the surface ectoderm results in increased accessibility of 1/3 of the regions opened during surface ectoderm differentiation. Conclusion: p63's ability to modify chromatin accessibility is dependent upon the underlying epigenetic landscape, and when it can modify the landscape, it does so by closing regions that become open during ectoderm differentiation.

2018-11-06 | GSE119996 | GEO

Expression profiles of miRNA derived from cells for ectoderm-biased substate of human pluripotent stem cells.

Project description:We established two different substates in human ES cell line, H9 cells, by changing the extracellular matrices. To examine a global miRNA expression comparison between the substate 1 and substate 2 cells, miRNA microarray was performed.

2019-08-22 | GSE123466 | GEO

Expression profiles of miRNA derived from exosomes for ectoderm-biased substate of human pluripotent stem cells.

2019-08-22 | GSE123470 | GEO

Cohesin HiChIP datasets of pluripotent and surface ectoderm cells with and without p63

Project description:Cohesin HiChIP datasets of pluripotent and surface ectoderm cells with and without p63

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mRNA expression profiles for ectoderm-biased substate of human pluripotent stem cells.

Project description:We established two different substates in human ES cell line, H9 cells, by changing the extracellular matrices. To examine a global gene expression comparison between the substate 1 and substate 2 cells, DNA microarray was performed.

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