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ChIP-seq of Runx3 in SFZ chondrocytes.

ABSTRACT: Purpose: To demonstrate Runx3's association with organizing the extracellular matrix in SFZ chondrocytes. Method: Fragment DNA samples were collected by using Anti-FLAG or IgG, from SFZ chondrocytes treated with lipofection of RUNX3-FLAG Results: 21,730 raw peaks met the peak calling criterion. Conclusions: By GO analysis, the extracellular structure organization and collagen fibril organization terms were the most significantly enriched.

ORGANISM(S): Mus musculus

PROVIDER: GSE157328 | GEO | 2020/09/03

REPOSITORIES: GEO

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RNA-seq of Runx3 cKO SFZ/DZ chondrocytes.

Project description:Purpose: To demonstrate Runx3's association with organizing the extracellular matrix in SFZ/DZ chondrocytes. Method: RNA samples were collected from SFZ/DZ chondrocytes of 5-day-old Col2a1-Cre;Runx3fl/fl and Runx3fl/fl mice. Results: 18 genes were up- or down-regulated by more than 2-fold in the Runx3 knockout in SFZ. Conclusions: However, genes organizing the extracellular matrix were down-regulated in Runx3 cKO DZ chondrocytes.

2020-09-04 | GSE157433 | GEO

ChIP-seq of Runx3 in SFZ chondrocytes.

Project description:ChIP-seq of Runx3 in SFZ chondrocytes.

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RNA-seq of Runx3 cKO SFZ/DZ chondrocytes.

Project description:RNA-seq of Runx3 cKO SFZ/DZ chondrocytes.

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Expression data from SFZ cells and costal chondrocytes

Project description:To understand difference between SFZ cells and costal chondrocytes, total RNAs from SFZ cells and costal chondrocytes were analyzed by microarray.

2023-09-06 | GSE242028 | GEO

mRNA-seq analysis of superficial zone (SFZ) and deeper layers (deep AC) of articular cartilage of adult rats

Project description:We compared gene expression profiles of SFZ and deep AC of articular cartilage through laser microdissection (LMD) using adhesive tape, linear amplification of mRNA, and mRNA-seq analysis. gene expression profiles of SFZ and deep AC obtained from the proximal tibia of two adult rats

2014-05-08 | E-GEOD-57377 | biostudies-arrayexpress

mRNA-seq analysis of superficial zone (SFZ) cells articular cartilage of 5-day-old mice

Project description:We compared gene expression profiles of SFZ cells of WT mice and Prg4KO mice using mRNA-seq analysis.

2021-04-20 | GSE148898 | GEO

RNA-seq in H1299 cell lines

Project description:Purpose: The goals of this study are to investigate the primary biological process of HNRNPC. Methods: Briefly, samples (H1299 cells transfected with control or HNRNPC shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: RNA-seq in H1299 cell lines revealed that HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity. Conclusions: HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity.

2022-03-30 | GSE199483 | GEO

The interactomes of RUNX1 and RUNX3 from Mus musculus T cells

Project description:Cellular binary fate decisions require the progeny to silence genes associated with the alternative fate. The major subsets of alpha:beta T cells have been extensively studied as a model system for fate decisions. While the transcription factor RUNX3 is required for the initiation of Cd4 silencing in CD8 T cell progenitors, it is not required to maintain the silencing of Cd4 and other helper T lineage genes. The other runt domain containing protein, RUNX1, silences Cd4 in an earlier T cell progenitor, but this silencing is reversed whereas the gene silencing after RUNX3 expression is not reverse. Therefore, we hypothesized that RUNX3 and not RUNX1 recruits other factors that maintains the silencing of helper T lineage genes in CD8 T cells. To this end, we performed a proteomics screen of RUNX1 and RUNX3 to determine candidate silencing factors.

2019-11-12 | PXD007511 | Pride

Expression data from superficial zone cells of articular cartilage (SFZ) cells treated with retinoic acid

Project description:To identify downstream transcription factors induced by retinoic acid, we stimulated SFZ cells with 10 μM retinoic acid for 24 hours and performed microarray analysis.

2018-12-17 | GSE107069 | GEO

RUNX3 Facilitates Growth of Ewing Sarcoma Cells

Project description:Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma. RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene. RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2. Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes. These results demonstrate an important role for RUNX3 in Ewing sarcoma. RNA-seq to compare transcriptiome of control A673 ewing sarcoma cells stably expression a non-target or RUNX3 shRNA

2014-05-01 | E-GEOD-56900 | biostudies-arrayexpress

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