Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling by 4SU-seq in mouse ESCs and ESC-derived neural progenitor cells.

ABSTRACT: Nascent RNA was metabolically labelled with 4SU in undifferentiated and ESC-derived neural progenitor cells (NPCs). 4SU incorporated RNA was isolated and deep-sequenced at day 0 (ESCs), 3, 5 and 7 of differentiation. NPC differentiation was monitored through expression of a GFP reporter insereted into the Sox1 locus (46C reporter ESC line; PMID: 12524553). The aim was to monitor changes in transcription as ESCs differentiate into NPCs and relate this to enhancer activity.

ORGANISM(S): Mus musculus

PROVIDER: GSE115774 | GEO | 2019/01/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Embryonic stem cells exhibit mRNA isoform-specific translational regulation

Project description:Investigation of the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC-derived neural precursor cells (NPCs) using polysome profiling coupled to RNA sequencing. Mouse ESCs were differentiated into Sox1-positive neural precursor cells (NPCs). One replicate of ESCs and NPCs were harvested and subjected to polysome fractionation. Fractions containing polysomes were purified and analysed by SOLiD sequencing. Expression levels in NPCs were compared to ESCs.

2016-01-26 | E-GEOD-73467 | biostudies-arrayexpress

Transcriptional profiling by 4SU-seq in mouse ESCs and ESC-derived neural progenitor cells.

Project description:Transcriptional profiling by 4SU-seq in mouse ESCs and ESC-derived neural progenitor cells.

| PRJNA475990 | ENA

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

Gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes

Project description:Differences of metabolism-related gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes were analyzed and successfully identified. Human ESCs and ESC-derived purified cardiomyocytes were used for this experiment.

2016-03-31 | E-GEOD-77518 | biostudies-arrayexpress

Expression data from embryonic stem cells (ESCs) and ESC-like cells

Project description:The transplantation of ESCs into living recipients causes teratoma formation which accompanies with several biological reactions in both the transplanted cells and recipient. Co-injection of ESCs with somatic cells that influence donor-recipient homogeneity can affect transcriptional profile of transplanted ESCs. We investigated global gene expression of parental ESCs and ESC-like cells derived from teratomas which were formed by different injection conditions to find transcriptional differences according to donor-recipient homogeneity and somatic cell co-injection. Parental ESCs or teratoma-derived ESC-like cells from different treatments were retrieved for RNA extraction and hybridization on Affymetrix microarrays.

2014-06-23 | E-GEOD-58725 | biostudies-arrayexpress

Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

Project description:ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets Three biological replicates each of ESCs and NPCs were prepared and assays using Affymetrix Gene Expression Arrays

2013-02-20 | E-GEOD-38850 | biostudies-arrayexpress

Gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes

Project description:Differences of metabolism-related gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes were analyzed and successfully identified.

2016-03-31 | GSE77518 | GEO

Expression data from embryonic stem cells (ESCs) and ESC-like cells

2014-06-23 | GSE58725 | GEO

Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

2013-02-20 | GSE38850 | 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

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