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-Gbx2-transfected 46C mouse embryonic stem cells

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE98387 | GEO | 2017/05/02

SECONDARY ACCESSION(S): PRJNA384974

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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-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-TERRA-transfected 46C Mouse Embryonic Stem Cells

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

| PRJNA407676 | ENA

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

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

Mouse ESC 46C replication analysis by repli-chip

Project description:Mouse ESC 46C replication timing has been assessed by repli-chip.

2017-07-28 | GSE95090 | GEO

Ptpb1 iCLIP in 46C mESCs and mNPCs

Project description:PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation. 46C mESCs and mNPCs were cross-linked at 100 mJ/cm2. Cell pellets were collected and flash-frozen for iCLIP library preparation. Libraries were subjected to 100 single-end RNA-sequencing.

2016-07-03 | E-GEOD-71178 | biostudies-arrayexpress

Splicing analyses of 46C mNPCs following PTBP depletion

Project description:PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation. 46C mESCs were differentiated in mNPCs. The mNPCs were treated with 10 nM control, Ptbp1, Ptbp2, or Ptbp1 and Ptbp2 siRNAs for 48 hours. The knockdowns were performed using 2 independent sets of siRNAs. Poly-A RNA was isolated for RNA-sequencing and splicing analyses.

2016-07-03 | E-GEOD-70985 | biostudies-arrayexpress

Splicing analyses of 46C mESCs following PTBP depletion

Project description:PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation. 46C mESCs were treated with 20 nM control, Ptbp1, Ptbp2, or Ptbp1 and Ptbp2 siRNAs for 72 hours. The knockdowns were performed using 2 independent sets of siRNAs, including one biological replicate. Poly-A RNA was isolated for RNA-sequencing and splicing analyses.

2016-07-03 | E-GEOD-71075 | biostudies-arrayexpress

RNA Microarray of 36H liver stages of Pb WT and Pb SSPELD Knock out parasites

Project description:Global gene expression profiling of P. berghei liver stages at 36h from WT and Pb SSPELD KO parasites to investigate the changes in RNA expression levels in Pb SSPELD parasites.

2016-09-01 | GSE72399 | GEO

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