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Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

ABSTRACT: Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

PROVIDER: PRJEB48247 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7133650_1.fastq.gz	Fastqsanger.gz
	ERR7133650_2.fastq.gz	Fastqsanger.gz
	ERR7133651_1.fastq.gz	Fastqsanger.gz
	ERR7133651_2.fastq.gz	Fastqsanger.gz
	ERR7133652_1.fastq.gz	Fastqsanger.gz

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Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

| PRJEB48248 | ENA

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

| PRJEB48249 | ENA

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

| PRJEB48250 | ENA

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

Project description:The aim of this experiment was to identify the RUNX2-dependent transcriptional program in thyroid cancer. To this end TPC1 cell line was infected with dCas9-KRAB and sgRNA targeting RUNX2 distal promoter or a non-targeting sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by mRNA-seq. Three replicates were analyzed.

2023-10-20 | E-MTAB-11049 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

Project description:The aim of the experiment was to explore the RUNX2 genomic functions in the papillary thyroid carcinoma. To this end, we performed Chromatin Immunoprecipitation followed by deep-sequencing using an antibody against RUNX2 in TPC1 thyroid cancer cell line, in order to define the genomic regions bound by this transcription factor.

2023-10-20 | E-MTAB-11051 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

Project description:We performed Chromatin Immunoprecipitation followed by deep-sequencing in TPC1 thyroid cancer cell line model, in order to identify the genomic elements enriched in RNA-Polymerase II, the enzymatic complex required for gene transcription. These data were integrated with RUNX2 genomic occupancy to map the RUNX2 responsive elements that are actively transcribed.

2023-10-20 | E-MTAB-11052 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

Project description:We performed Chromatin Immunoprecipitation followed by deep-sequencing in TPC1 thyroid cancer cell line model, in order to profile the genomic distribution of H3K27ac, H3K4me1 and H3K4me3, epigenetic markers of chromatin functional status. These data were integrated with RUNX2 genomic occupancy to define the nature and the activation status of the RUNX2-associated regions.

2023-10-20 | E-MTAB-11050 | biostudies-arrayexpress

RNA-seq of thyroid cancer cell line upon silencing of RAIN, a RUNX2 associated intergenic lncRNA, and RUNX2

Project description:The aim of this experiment was to identify the RUNX2- and RAIN-dependent transcriptional program in thyroid cancer. TPC1 and MDA-T41 cell line were infected with dCas9-KRAB and sgRNA targeting the gene of interest (RAIN or RUNX2 respectively) or a non-targeting (NT) sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by total RNA-seq.

2024-09-12 | E-MTAB-13777 | biostudies-arrayexpress

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Project description:The vertebrate skeleton is mostly composed of three specific cell types: immature chondrocytes (IMM), mature (hypertrophic) chondrocytes (MAT), and osteoblasts (OST). These three cell types are distinct, but they also share the expression of many genes. This overlapping gene expression can be attributed to two transcription factors, SOX9 and RUNX2, which operate near the top of hierarchy of the gene regulatory network (GRN) underlying IMM, MAT, and OST. Sox9 drives IMM differentiation, whereas Runx2 regulates OST differentiation. Importantly, MAT do not form without the function of either Sox9 or Runx2, but little is known about mechanisms of GRN regulation in MAT. During MAT differentiation, the expression of Runx2 increases, and many genes regulated by this transcription such as Spp1, Mef2c, Ibsp, and Alpl are activated. To understand regulatory control of gene expression in mature chondrocytes, ChIP-seq experiments were performed using the mouse chondrogenic cell line ATDC5. These experiments identified in vitro RUNX2 binding sites at different stages of chondrogenesis. RUNX2 appeared to bind in most genes enriched in MAT at both day 3 of differentiation. The ChIP-seq analyses presented here verified the molecular mechanisms predicted here to regulate transcription of the many genomic loci in MAT, proving more insight into regulatory control during cartilage maturation.

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