Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Repeat elements study in pluripotent stem cells [expression array]

ABSTRACT: We surveyed RNA-Seq data to identify those TEs that are transcriptionally active uniquely in human pluripotent cells. We identified one endogenous retrovirus (HERV-H) family, uniquely found in primates as being unusually abundant in the transcriptome. The microarray data provided is to support our human naive cell hypothesis. Total of 18 samples of the human ESC line H9 were analyzed for gene expression.

ORGANISM(S): Homo sapiens

SUBMITTER: Gangcai Xie

PROVIDER: E-GEOD-54725 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

repeat elements study in pluripotent stem cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-09 | E-GEOD-54726 | biostudies-arrayexpress

Repeat elements study in pluripotent stem cells [RNA-seq]

Project description:We surveyed RNA-Seq data to identify those TEs that are transcriptionally active uniquely in human pluripotent cells. We identified one endogenous retrovirus (HERV-H) family, uniquely found in primates as being unusually abundant in the transcriptome. Poly(A)+ RNA extraction and further sequencing library construction was done for two types of cells (iPS, HFF-1) and hiPSC-derived embryoid bodies following Illumina TruSeq RNA Sample Preparation Kit protocol, which was further sequenced on Illumina HiSeq machine with single-end 101 cycles.

2014-10-09 | E-GEOD-44646 | biostudies-arrayexpress

Determination of genes affected by HERVH depletion

Project description:The unique cellular state of embryonic stem cells is maintained by pluripotency-associated transcription factors such as OCT4. The transcriptional regulatory circuitries between human and mouse pluripotent stem cells exhibit notable differences. Transposable elements have altered the pluripotency network by contributing new cis-regulatory elements to mammalian genomes. In our study, we found that the expression of HERVH is enriched in human embryonic stem cells (hESCs) and depletion of HERVH in hESCs induced differentiation. To confirm the differentiation phenotype and identify potential downstream target genes of HERVH, we conducted the microarray analysis on hESCs treated with control shRNA against Luciferase and shRNA against HERVH. Total RNA was extracted from cells treated with control shRNA or HERVH shRNA for 5 days. 3 replicates each.

2014-03-30 | E-GEOD-42430 | biostudies-arrayexpress

Proteomic investigation of the effect of DAP5 knock-down on human embryonic stem cells

Project description:We performed a deep mass-spec analysis to determine DAP5 proteomic signature on human embryonic stem cells (hESCs) by evaluating the steady state proteins level on DAP5-KD and NT control cells.

2022-08-10 | PXD030717 | Pride

Transcriptional profiling by single cell-RNA sequencing of HARA cells according to Calbindin and HERVH-LTR7 activity

Project description:The purpose of this study to examine the effect of Calbindin expression, driven by an upstream HERVH LTR (human endogenous retrovirus H long terminal repeat), in HARA squamous lung cancer cells. Parental HARA cells, Calbindin-deficient HARA 3D5 cells, HARA.LTR7-GFP+ and HARA.LTR7-GFP- cells were compared and were processed as a single batch, using the 10× Genomics Chromium platform.

2023-08-01 | E-MTAB-11550 | biostudies-arrayexpress

RNA-Seq after knockdown of the endogeneous retrovirus HERVH in human embryonic stem cells

Project description:Human endogenous retrovirus subfamily H (HERVH) is a class of transposable elements whose members are expressed preferentially in human pluripotent stem cells. Here, we report that the long-terminal repeat regions of HERVH function as enhancers which are regulated by OCT4. Strikingly, we found that HERVH is a nuclear-localized long non-coding RNA that is required to maintain the undifferentiated state of human embryonic stem cells. Furthermore, we showed that HERVH is associated with OCT4 and co-activators such as P300, CBP and mediator subunits. Together, these results uncover a new and unexpected role of species-specific transposable elements in specifying the pluripotency of human cells.

2014-03-30 | E-MTAB-2072 | biostudies-arrayexpress

Repeat elements study in pluripotent stem cells [RNA-seq]

2014-10-09 | GSE44646 | GEO

Repeat elements study in pluripotent stem cells [expression array]

2014-10-09 | GSE54725 | GEO

Role of DNMT3B in the regulation of early neural and neural crest specifiers

Project description:The de novo DNA methyltransferase DNMT3B functions in establishing DNA methylation patterns during development. We performed RNAi knockdown of DNMT3B in human embryonic stem cells (ESCs) in order to investigate the mechanistic contribution of DNMT3B on DNA methylation and early neuronal differentiation. Genome-wide analyses of DNA methylation by MethylC-seq identified novel regions of hypomethylation in the DNMT3B knockdowns along the X chromosome as well as pericentromeric regions, rather than changes to specific dysregulated gene promoters. While DNMT3B was not required for early neuroepithelium specification, DNMT3B deficient neuroepithelium exhibited accelerated maturation with earlier expression of mature neuronal markers (such as NEUROD1) and early neuronal regional specifiers (such as neural crest) relative to normal ESCs. Our results suggest that DNMT3B mediates large-scale methylation patterns in human ESCs and that DNMT3B deficiency alters the timing of neuronal maturational differentiation in human neuronal cultures. Examined DNA methylation in human embryonic stem cells, both with and without DNMT3B knockdown

2012-03-27 | E-GEOD-32268 | biostudies-arrayexpress

Epigenetic therapy for Friedreich ataxia.

Project description:We set out to investigate whether a histone deacetylase inhibitor (HDACi) would be effective in an in vitro model for the neurodegenerative disease Friedreich ataxia (FRDA) and to evaluate safety and surrogate markers of efficacy in a phase I clinical trial in patients. In the neuronal cell model, HDACi 109/RG2833 increases FXN mRNA levels and frataxin protein, with concomitant changes in the epigenetic state of the gene. Chromatin signatures indicate that histone H3 lysine 9 is a key residue for gene silencing through methylation and reactivation through acetylation, mediated by the HDACi. Drug treatment in FRDA patients demonstrated increased FXN mRNA and H3 lysine 9 acetylation in peripheral blood mononuclear cells. No safety issues were encountered. We used a human FRDA neuronal cell model, derived from patient induced pluripotent stem cells, to determine the efficacy of a 2-aminobenzamide HDACi (109) as a modulator of FXN gene expression and chromatin histone modifications. FRDA patients were dosed in 4 cohorts, ranging from 30mg/day to 240mg/day of the formulated drug product of HDACi 109, RG2833. Patients were monitored for adverse effects as well as for increases in FXN mRNA, frataxin protein, and chromatin modification in blood cells. Gene expression profiles were obtained using the Illumina HT12v4 Gene Expression BeadArray.

2015-01-29 | E-GEOD-65399 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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