Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Anti-NR2F1 scCUT&Tag on FAC-sorted Isl1MN-GFP rhombomere 4 neurons from wildtype and HCFP1 Fam5snv/snv E10.5 mouse embryos

ABSTRACT: We found hereditary congenital facial paralysis type 1 (HCFP1) is caused by variants that duplicate or change cis regulatory elements (cREs) controlling the neuronal expression of the GATA2 transcription factor. The single nucleotide variants (SNVs) alter a previously uncharacterized cis regulatory element (we named cRE2). A subset of these variants disrupted a consensus sequence for the COUP transcription factor family (NR2F1 and NR2F2). We performed low-input scCUT&Tag with antibodies against NR2F1 and found it bound to the predicted cRE2 sequence in embryonic mouse rhombomere 4 motor neurons in vivo. We generated an HCFP1 SNV mouse model that harbored Mm10:Chr6:88,224,892 A>G in the NR2F1 binding site (Fam5snv/snv) and found it disrupted NR2F1 binding in vivo.

ORGANISM(S): Mus musculus

PROVIDER: GSE223271 | GEO | 2023/04/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Anti-NR2F1 scCUT&Tag on FAC-sorted Isl1MN-GFP rhombomere 4 neurons from wildtype and HCFP1 Fam5snv/snv E10.5 mouse embryos

Project description:Anti-NR2F1 scCUT&Tag on FAC-sorted Isl1MN-GFP rhombomere 4 neurons from wildtype and HCFP1 Fam5snv/snv E10.5 mouse embryos

| PRJNA925500 | ENA

Effect of PTCHD1 SNV and truncating variants on gene expression during differentiation of iPSCs to neural progenitor cells

Project description:To investigate whether a SNV in the gene PTCHD1 was disease causative, we introduced the variant to KOLF-2 iPSCs via CRISPR/Cas9 homology directed repair. Three experimentally matched SNV and WT clones and two clones with truncating mutations were generated, and neural induction was induced. We then performed gene expression profiling analysis using data obtained from RNA-seq of these cells at two timepoints (day 0 and day 24 of neural induction).

2023-11-19 | GSE227711 | GEO

SNV microarray data from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al

Project description:SNV microarray data from eleven family members in a family with high rates of cardiomyopathy Source name refers to patient position in pedigree from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al

2018-10-27 | GSE121844 | GEO

Evaluating Differential Tropism, Pathogenesis, and Antiviral Agents of Hemorrhagic Fever Renal Syndrome and Cardiopulmonary Syndrome Causative Hantaviruses: Andes virus (ANDV), Sin Nombre virus (SNV), and Hantaan virus (HTNV)

Project description:We report RNAseq analysis of control, calu3, astrocytes and cardiomyocytes cells under uninfected (mock) and Andes virus (ANDV), Sin Nombre virus (SNV), Hantaan virus (HTNV) infected and drug (synthetic 6AZA and Favipiravir, herbal Silymarin and Urolithin B) treated conditions

2024-05-16 | GSE232641 | GEO

Effect of PTCHD1 SNV and truncating variants on gene expression during differentiation of iPSCs to neural progenitor cells

Project description:Effect of PTCHD1 SNV and truncating variants on gene expression during differentiation of iPSCs to neural progenitor cells

| PRJNA946696 | ENA

Germline snv g.vcf for EGAS00001004572 - samples

Project description:Bulk Germline snv vcfs from haplotypecaller analysis in EGAS00001004572

| EGAD00001006910 | EGA

Genome-wide analysis of p300, H3K4me3, H3K4me1, H3K27me3 and H3K27ac in in vitro differentiated human neural crest cells (hNCC)

Project description:Combining an in vitro hNCC differentiation protocol with epigenomic profiling, we provide the first whole-genome characterization of cis-regulatory elements in this highly relevant cell type. With this data at hand, we have characterized the chromatin state and dynamics of all human gene promoters during the course of NCC in vitro differentiation. Most importantly, we have identified a large cohort of active and NCC-specific enhancers, which we showed to be functionally relevant in vivo, in the context of embryonic development. Finally, through sequence analysis of the identified NCC enhancers, we uncovered the orphan nuclear receptors NR2F1 and NR2F2 as novel hNCC transcriptional regulators both in vitro and in vivo. Genome-wide analysis of p300, H3K4me3, H3K4me1, H3K27me3, H3K27ac, NR2F1, NR2F2 and TFAP2A in in vitro differentiated human neural crest cells (hNCC)

2012-09-13 | E-GEOD-28874 | biostudies-arrayexpress

Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest

Project description:Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes. Histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), chromatin modifiers (p300), transcription factors (NR2F1, TFAP2A), chromatin accessibility (ATACseq) and gene expression (RNAseq) were assayed in CNCCs derived from iPSCs/ESCs from 2 chimpanzee and 3 human individuals.

2015-09-11 | E-GEOD-70751 | biostudies-arrayexpress

Strelka somatic snv vcfs for EGAS00001004572 - samples

Project description:Bulk Strelka somatic snv vcfs from tumour-normal analysis in EGAS00001004572

| EGAD00001006907 | EGA

Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons

Project description:BACKGROUND: Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting ‘normal’ mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes In this study we amplified mt-genomes from 1,645 single mitochondria (mts) isolated from mouse single astrocytes and neurons to 1. determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome,2. assess differences in mtDNA SNVs between neurons and astrocytes, and 3. Study cosegregation of variants in the mouse mtDNA. RESULTS: 1. The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. 2. Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G>A and 9419:C>T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. 3. Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. CONCLUSION: This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.

2024-06-24 | GSE218122 | 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