Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vivo genome-wide chromatin immunoprecipitation for the chondrogenic transcription factors, Sox9, Sox5 and Sox6

ABSTRACT: Tissue ChIP-seq was performed on transcription factor Sox5, Sox6 and Sox9 using limbs and tails from E13.5 mouse embryos to find their in vivo binding sites in the genome

ORGANISM(S): Mus musculus

PROVIDER: GSE33419 | GEO | 2017/06/15

SECONDARY ACCESSION(S): PRJNA148915

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sox5 and Sox6 direct a cardiac adaptive response to pressure overload

Project description:Rationale: We previously demonstrated that the transcription factor Sox6 regulates skeletal muscle biology by determining myofiber composition and muscle performance. Although the role of Sox6 and Sox5, its closest paralog, has not been ascertained in the heart, genome-wide association studies linked both Sox5 and Sox6 to cardiovascular disease. Objective: This study identifies the role of Sox5 and Sox6 in the adult mammalian heart under normal and stress conditions. Methods and Results: Using Sox5 and Sox6 cardiac-specific and Sox5 conduction system-specific knockout mice, we investigated the role of the two transcription factors in the heart under normal conditions and during cardiac stress. Sox5/6-deficient (DKO) mice displayed blunted cardiac contractility, which was present in Sox5 but not Sox6 single KO mice. DKO mice had a mild reduction in blood pressure, and conduction-specific knockout of Sox5 resulted in a reduced heart rate at baseline. After cardiac pressure overload, DKO mice showed increased lethality compared to control mice and were more prone to develop heart failure. We performed RNA deep sequencing in ventricles from DKO and control mice to identify potential Sox5/6 target genes and found altered expression of genes encoding regulators of calcium handling and cation transporters. Patch-clamping in isolated cardiomyocytes revealed shortened action potential duration in Sox5 KO cells. Conclusions: Unlike in skeletal muscle, our results suggest Sox5 but not Sox6 to be a major regulator of cardiac function and rhythm. Sox5 is essential to preserve cardiac function under normal conditions by maintaining contractility and to prevent cardiac failure after pressure overload.

2018-08-05 | GSE60538 | GEO

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (ChIP-Seq)

Project description:SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio. ChIP-seq for SOX9, SOX6 and histone modifications were carried out using RCS cells

2015-06-23 | E-GEOD-70143 | biostudies-arrayexpress

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq)

Project description:SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio. RNAs were isolated from three bioogical replicatse of rat chondrosarcoma (RCS) cells and rib samples for RNA-seq experiments.

2015-06-23 | E-GEOD-70142 | biostudies-arrayexpress

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (ChIP-Seq)

Project description:SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.

2015-06-23 | GSE70143 | GEO

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq)

Project description:SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.

2015-06-23 | GSE70142 | GEO

Genome-wide profiling of the Sox chondrogenic trio at E13.5

Project description:Transgenic mice tagged with EGFP under the control of the endogenous Sox5, Sox6 and Sox9 promoter were used. E13.5 transgenic embryos were enriched for the skeletal elements and FACS was used to isolate the Sox5/6/9-expressing cells which were used for comparative expression profiling between wildtype and knockout.

2017-06-10 | GSE33173 | GEO

RNA-seq of SOX5 overexpressing primary human neuronal progenitors

Project description:Purpose: The goal of this study was to assess gene expression changes in neurons overexpressing SOX5 using human primary neuronal culture system. Methods: 6 samples each from control GFP and SOX5 overexpressing neurons were used to isolate total RNA using miRNeasy kit, Qiagen. We performed rRNA-depleted 69bp paired end stranded RNA-seq on neurons overexpressing either GFP or SOX5 tagged with GFP. Overexpression of SOX5 in neurons validated that a significant proportion of Attenuated cortical patterning (ACP) genes are regulated by SOX5, and that predicted SOX5 targets exhibit a net downregulation, consist with its repressive function. This supports the prediction that attenuated patterning of SOX5 between cortical regions contributes to direct alterations in SOX5 targets and likely to indirect alterations in SOX5 non-targets in the ACP set. delpleted 69 bp stranded RNA-seq in

2016-11-17 | GSE89057 | GEO

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis.

Project description:SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We use here genome-wide approaches to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio. Using the RCS cell line as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes, we uncover that SOX6 and SOX9 bind thousands of genomic sites, frequently and most efficiently near each other. SOX9 recognizes pairs of inverted SOX motifs, whereas SOX6 favors pairs of tandem SOX motifs. The SOX proteins primarily target enhancers. While binding to a small fraction of typical enhancers, they bind multiple sites on almost all super-enhancers (SEs) present in RCS cells. These SEs are predominantly linked to cartilage-specific genes. The SOX proteins effectively work together to activate these SEs and are required for in vivo expression of their associated genes. These genes encode key regulatory factors, including the SOX trio proteins, and all essential cartilage extracellular matrix components. Chst11, Fgfr3, Runx2 and Runx3 are among many other newly identified SOX trio targets. SOX9 and SOX5/SOX6 thus cooperate genome-wide, primarily through SEs, to implement the growth plate chondrocyte differentiation program.

| S-EPMC4787819 | biostudies-other

RNA-seq data from mouse newborn rib chondrocytes

Project description:To understand the targets of Sox5, Sox6 and Sox9, we overexpressed Sox5/6/9 in mouse newborn rib chondrocytes and expression analysis by RNA-seq.

2021-01-20 | GSE155118 | GEO

CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

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