Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Platform for Induction and Maintenance of Transgene-Free hiPSCs Resembling Ground State Pluripotent Stem Cells

ABSTRACT: The purpose of this series of experiments is to identify copy number variations, duplications, deletions and regions of homozygosity in human induced pluripotent stem (hiPSC) cell lines. Genomic DNA of human induced pluripotent stem cell lines are extracted and hybridized to Agilent aCGH+SNP microarray, using genotyped Agilent Reference DNA as common reference. Differences and similarities between fibroblast and stem cell lines will be revealed.

ORGANISM(S): Homo sapiens

SUBMITTER: Bahram Valamehr

PROVIDER: E-GEOD-54080 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Platform for Induction and Maintenance of Transgene-Free hiPSCs Resembling Ground State Pluripotent Stem Cells

Project description:The purpose of this series of experiments is to identify copy number variations, duplications, deletions and regions of homozygosity in human induced pluripotent stem (hiPSC) cell lines.

2014-03-03 | GSE54080 | GEO

Platform for induction and maintenance of transgene-free hiPSCs resembling ground state pluripotent stem cells.

Project description:Cell banking, disease modeling, and cell therapy applications have placed increasing demands on hiPSC technology. Specifically, the high-throughput derivation of footprint-free hiPSCs and their expansion in systems that allow scaled production remains technically challenging. Here, we describe a platform for the rapid, parallel generation, selection, and expansion of hiPSCs using small molecule pathway inhibitors in stage-specific media compositions. The platform supported efficient and expedited episomal reprogramming using just OCT4/SOX2/SV40LT combination (0.5%-4.0%, between days 12 and 16) in a completely feeder-free environment. The resulting hiPSCs are transgene-free, readily cultured, and expanded as single cells while maintaining a homogeneous and genomically stable pluripotent population. hiPSCs generated or maintained in the media compositions described exhibit properties associated with the ground state of pluripotency. The simplicity and robustness of the system allow for the high-throughput generation and rapid expansion of a uniform hiPSC product that is applicable to industrial and clinical-grade use.

| S-EPMC3964282 | biostudies-literature

CGH + SNP microarray analysis in consanguineous family with ovarian dysgenesis

Project description:homozygosity mapping in a family with ovarian failure Two affected and four unafected siblings from consanguineous family were studied to identify shared regions of homozygosity in affected females with gonadal dysgenesis

2014-10-16 | E-GEOD-62347 | biostudies-arrayexpress

ChIP-seq in MEG3+ and MEG3- hIPSCs

Project description:In this experiment we sought to identify region with differential PRC2, JARID2, and H3K27me3 occupancy in human induced pluripotent stem cell lines with silenced or expressed MEG3 locus to indirectly determine the effect of this ncRNA on PRC2 function. 8 hIPSC lines, 5 MEG3+ and 3 MEG3-; ChIP-seq for EZH2, JARID2, and H3K27me3. Some done in replicates.

2013-12-25 | E-GEOD-48516 | biostudies-arrayexpress

Alginate encapsulation of differentiating hiPSCs

Project description:Here we characterize the impact of cell confinement on the pancreatic islet signature during the guided differentiation of alginate encapsulated human induced pluripotent stem cells.

2020-02-12 | PXD012704 | Pride

Resetting Transcription Factor Control Circuitry Towards Ground State Pluripotency In Human

Project description:Current human pluripotent stem cells lack the transcription factor circuitry that governs the ground state of mouse embryonic stem cells (ESC). Here we report that short-term expression of two components, NANOG and KLF2, is sufficient to ignite other elements of the network and reset the human pluripotent state. Inhibition of ERK and protein kinase C signalling sustains a transgene-independent rewired state. Reset cells self-renew continuously without ERK signalling, are phenotypically stable and karyotypically intact. They differentiate in vitro and form teratomas in vivo. Metabolism is reprogrammed in reset cells with activation of mitochondrial respiration as in ESC. DNA methylation is dramatically reduced and transcriptome state is globally realigned across multiple cell lines. Depletion of ground state transcription factors, TFCP2L1 or KLF4 has marginal impact on conventional human pluripotent stem cells, but collapses the reset state. These findings demonstrate feasibility of installing and propagating functional control circuitry for ground state pluripotency in human cells. DNA methylation analysis in Conventional and Reset human embryonic stem cells by whole genome bisulfite sequencing, in triplicate, using the Illumina platform

2014-09-10 | E-GEOD-60945 | biostudies-arrayexpress

ChIP-seq in MEG3+ and MEG3- hIPSCs

2013-12-25 | GSE48516 | GEO

Sox2 Levels Define Pluripotent Ground States and Reprogramming Potential

Project description:Pluripotent stem cell lines derived from embryos of different stages have distinct pluripotent ground states, but similar levels of the transcription factor Oct4. Epiblast-derived pluripotent stem cells (EpiSCs), in contrast to embryonic stem (ES) cells, cannot form chimeras. We show that EpiSCs express lower levels of the transcription factors Sox2 and Klf4 than ES cells and have limited reprogramming potential, as shown by cell fusion. Sox2 overexpression dramatically increases the reprogramming potential, chimera formation, and germline contribution of EpiSCs. Therefore, although Oct4 is essential for reprogramming, the level of Sox2 defines both the reprogramming capability and the pluripotent ground states.

2010-12-31 | GSE15358 | GEO

The growth factor environment defines distinct pluripotent ground states in novel blastocyst derived stem cells

Project description:Pluripotent stem cell lines can be derived from blastocyst embryos, which yield embryonic stem cell lines (ES cells), as well as the post-implantation epiblast, which gives rise to epiblast stem cell lines (EpiSCs). Remarkably, ES cells and EpiSCs display profound differences in the combination of growth factors that maintain their pluripotent state. Molecular and functional differences between these two stem cell types demonstrate that the tissue of origin and/or the growth factor milieu may be important determinants of the stem cell identity. We explored how developmental stage of the tissue of origin and culture growth factor conditions affect the stem cell pluripotent state. Our findings reveal that novel stem cell lines can be generated from blastocyst embryos with unique functional and molecular properties. We demonstrate that the culture growth factor environment and cell-cell interaction play a critical role in defining several unique and stable stem cell ground states. Keywords: Clonal analysis of FAB-SC gene expression Cell type characterization - 3 separate single cell clones

2010-05-17 | E-GEOD-12519 | biostudies-arrayexpress

The NIH Human Pluripotent Stem Cell Database (Agilent, cgh)

Project description:Array comparative genomic hybridization was performed on DNA samples matched to the RNA samples included in the NIH Human Pluripotent Stem Cell Database (Series GSE32923). Twenty two undifferentiated human embryonic stem cell lines were analyzed. Expanded descriptions of methods used are available at: http://stemcelldb.nih.gov. 22 hybridizations: 10 human male ESC (UNDIFFerentiated) lines vs human male reference, 12 human female ESC (UNDIFFerentiated) lines vs human female reference.

2012-10-31 | E-GEOD-35735 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data