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

Notch engagement by Jag1 clusters on the nanoscale suggests a force-independent mode of activation

ABSTRACT: The Notch signaling pathway is a cell-cell communication system with fundamental roles in embryonic development and the nervous system, including neural stem cell proliferation and differentiation. To investigate the multivalency effect of ligands on the activation of the Notch receptor, we treated iPSc-derived neuroepithelial stem-like (lt-NES) cells with different Jag1 nanopatterns on DNA origami nanostructures.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-12439 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP143136

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (3)

Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established nerual stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 3 in published article. Single cell raw data files for experiments are not available for public download.

2019-10-24 | E-MTAB-8383 | biostudies-arrayexpress

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (2)

Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 2 in published article. Single cell raw data files for experiments are not available for public download.

2019-10-24 | E-MTAB-8379 | biostudies-arrayexpress

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (1)

Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 4 in published article. Single cell raw data files for experiments were not made available.

2019-10-24 | E-MTAB-8363 | biostudies-arrayexpress

scRNA-seq for mEpiSCs (epiblast stem cells) differentiated to posterior primitive streak (PPS) in vitro, in a monolayer

Project description:EpiSCs established from murine epiblast were differentiated to posterior primitive streak (PPS) and analyzed using scRNA-seq to investigate identity and homogeneity of the resulting population.

2022-11-30 | E-MTAB-12106 | biostudies-arrayexpress

scRNA-seq of mouse EpiSCs (epiblast stem cells) differentiated to extraembryonic mesoderm in vitro, in a monolayer

Project description:EpiSCs derived from epiblast of a gastrulating embryo differentiated towards extraembryonic mesoderm to test the efficiency of the differentiation protocol and identity and homogeneity of the resulting cell population.

2022-11-30 | E-MTAB-12107 | biostudies-arrayexpress

CUT&RUN experiment at four time points in HEK293T and hESC cells, assessing the time-resolved response of β-catenin genomic occupancy upon Wnt signaling activation

Project description:Wnt/β-catenin signaling is a highly organized biochemical cascade that triggers a gene expression program in the signal-receiving cell. The Wnt/β-catenin-driven transcriptional response is involved in virtually all cellular processes during development, homeostasis, and its deregulation causes human disease. However, outstanding questions remain unanswered. A first question concerns cell-specificity: how this response is integrated into lineage-specific choices is still unknown. A second question concerns time: it is not known whether β-catenin associates with its targets simultaneously or in a time-dependent fashion. For instance, while TCF/LEF and other components of the Wnt transcriptional complex are constitutively associated with the chromatin, it is β-catenin arrival, upon Wnt induction, that launches target genes transcription. Therefore, discovering the dynamics of the genome-wide β-catenin binding pattern is required to unambiguously define the direct targets of Wnt signaling To address these questions, we realized a time-resolved atlas of β-catenin genome-wide occupancy in two human cell types, human embryonic kidney cells 293T (HEK293T) and human embryonic stem cells (hESCs). To this end, we treated HEK293T and hESCs with the GSK3 inhibitor/Wnt activator CHIR99021 (10 mM) for 3 days, and assessed β-catenin binding via CUT&RUN-LoV-U (Zambanini et al., 2022) 90 minutes, 4 hours, 24 hours and 3 days after the onset of the stimulation. This approach allowed us to establish that β-catenin repositions to different genomic loci along stimulation time, showing that a definition of Wnt target genes must take into account the time-dimension. Moreover, β-catenin physical targets are largely cell-type specific, as only a subset of them is present across the examined contexts.

2022-09-30 | E-MTAB-12077 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - Organoid

Project description:Individual TFs were overexpressed in fetal lung tip organoids from a doxycycline-inducible construct for 3 days, and organoids were maintained in the self-renewing (tip cell-promoting) medium throughout to rigorously assay the lineage-determining competence of the TF, followed by scRNA-seq. ASCL1, NEUROD1, and NEUROG3 were selected as key neuroendocrine regulators. We also selected the GHRL+ NE-specific RFX6 and NKX2.2, the pan-NE PROX1, and, as controls, the basal cell-specific TFs DeltaNTP63, TFAP2A, PAX9, and mNeonGreen-3xNLS.

2022-01-27 | E-MTAB-11267 | biostudies-arrayexpress

RNA-seq analysis of neonatal mouse cochlear supporting cells [Treated AK]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6 after inhibition of the Notch signaling pathway. Cochleas from postnatal day 0 and postnatal day 5 were cultured for 24 hours in the gamma secretase inhibitor DAPT or DMSO as a vehicle control. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 0+24 hours culture and postnatal day 5 + 24 hours culture. (corresponding to P1 and P6). mRNA profiles of P0 and P5 supporting cells (GFP+) and all other cochlear cell types (GFP-) treated with DAPT or DMSO, two replicates each, were generated by deep sequencing using Illumna TruSeq.

2016-07-01 | E-GEOD-83340 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in high glucose condition

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in a high glucose concentration media

2024-08-31 | E-MTAB-14308 | biostudies-arrayexpress