Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-TERRA-transfected 46C Mouse Embryonic Stem Cells

ABSTRACT: Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-TERRA-transfected 46C Mouse Embryonic Stem Cells

PROVIDER: PRJNA407676 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-TERRA-transfected 46C Mouse Embryonic Stem Cells

Project description:Next-generation sequencing facilitates quantitative analysis of transcriptomes in 46C mouse embryonic stem cells overexpressing PB-TERRA or PB empty vector at gene expression level. Results provide important information of the response of up-regulating TERRA, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells.

2017-09-18 | GSE103933 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-ID2-transfected 46C mouse embryonic stem cells

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in 46C mouse embryonic stem cells overexpressing PB-ID2 or PB empty vector at gene expression level. Results provide important information of the response of up-regulating ID2, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells

2017-05-11 | GSE98759 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-Gbx2-transfected 46C mouse embryonic stem cells

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in 46C mouse embryonic stem cells overexpressing PB-Gbx2 or PB empty vector at gene expression level. Results provide important information of the response of up-regulating Gbx2, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells

2017-05-02 | GSE98387 | GEO

Investigating the role of Lef1 in mouse embryonic stem cells.

Project description:Genome-wide analysis of gene expression in piggybac empty vector and piggybac-lef1 transfected mouse embryonic stem cells (46C mouse ESCs) Analysis of genes regulated by lef1, and we found that lef1 acts biphasically in mouse embryonic stem cells. Total RNA obtained from empty vector (PB)-transfected 46 ESCs or different states (passage 2 and passage 5) of lef1-transfected (PB-Lef1 P2, PB-Lef1 P5) 46C mouse ESCs.

2016-01-29 | E-GEOD-77330 | biostudies-arrayexpress

Functional characterization of the TERRA transcriptome at damaged telomeres

Project description:We characterize the TERRA transcriptome at normal and TRF2-depleted telomeres by RNA-seq and we demonstrate that TERRA upregulation is occurring at all transcribed telomeres upon depletion of TRF2. RNA-sequencing of HeLa mRNA, 4 samples: with or without TERRA enrichment by IP (respectively "IP" and "input"), with or without TFR-2 knock-down (respectively "_T" and "_EV").

2014-10-31 | E-GEOD-56727 | biostudies-arrayexpress

TERRA RNA antagonizes ATRX and protects telomeres

Project description:Through an integration of genomic and proteomic approaches to advance understanding of long noncoding RNAs, we investigate the function of the telomeric transcript, TERRA. By identifying thousands of TERRA target sites in the mouse genome, we demonstrate that TERRA can bind both in cis to telomeres and in trans to genic targets. We then define a large network of interacting proteins, including epigenetic factors, telomeric proteins, and the RNA helicase, ATRX. TERRA and ATRX share hundreds of target genes and are functionally antagonistic at these loci: whereas TERRA activates, ATRX represses gene expression. At telomeres, TERRA competes with telomeric DNA for ATRX binding, suppresses ATRX localization, and ensures telomeric stability. Depleting TERRA increases telomerase activity and induces telomeric pathologies, including formation of telomere-induced DNA damage foci and loss or duplication of telomeric sequences. We conclude that TERRA functions as an epigenomic modulator in trans and as an essential regulator of telomeres in cis.

2017-06-29 | GSE79180 | GEO

PAR-TERRA RNA directs homologous sex chromosome pairing

Project description:In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a ‘tetrad’ of pairwise homologous interactions (Xic–Xic, PAR–PAR, and Xic–PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a ‘constrained diffusion model’ in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.

2017-07-10 | GSE69887 | GEO

Mus musculus

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-Gbx2-transfected 46C mouse embryonic stem cells

| PRJNA384974 | ENA

Mus musculus

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-ID2-transfected 46C mouse embryonic stem cells

| PRJNA386151 | ENA

TERRA regulates DNA G-quadruplex formation and ATRX loading on chromatin

Project description:The genome consists of non-B-DNA structures such as G-quadruplexes (G4) that are involved in the regulation of genome stability and transcription. Telomeric-repeat containing RNA (TERRA) is capable of folding into G-quadruplex and interacting with chromatin remodeler ATRX. Here we show that TERRA modulates ATRX occupancy on repetitive sequences and over genes, and maintains DNA G-quadruplex structures at TERRA target and non-target sites in mouse embryonic stem cells. TERRA prevents ATRX from binding to subtelomeric regions and represses H3K9me3 formation. G4 ChIP-seq reveals that G4 abundance decreases at accessible chromatin regions, particularly at transcription start sites (TSS) after TERRA depletion; such G4 reduction at TSS is associated with elevated ATRX occupancy and differentially expressed genes. Loss of ATRX alleviates the effect of gene repression caused by TERRA depletion. Immunostaining analyses demonstrate that knockdown of TERRA diminishes DNA G4 signals, whereas silencing ATRX elevates G4 formation. Our results uncover an epigenetic regulation by TERRA that sequesters ATRX and preserves DNA G4 structures.

2022-11-09 | GSE194038 | GEO

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