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RNA-seq analysis of equine tenocytes exposed to siRNA targeting scleraxis (Scx) to identify novel targets of Scx-mediated mechanotransduction

ABSTRACT: RNA-seq analysis of equine tenocytes exposed to siRNA targeting scleraxis (Scx) to identify novel targets of Scx-mediated mechanotransduction

PROVIDER: PRJNA433994 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6721560_1.fastq.gz	Fastqsanger.gz
	SRR6721560_2.fastq.gz	Fastqsanger.gz
	SRR6721561_1.fastq.gz	Fastqsanger.gz
	SRR6721561_2.fastq.gz	Fastqsanger.gz
	SRR6721556_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of equine tenocytes exposed to siRNA targeting scleraxis (Scx) to identify novel targets of Scx-mediated mechanotransduction

Project description:Equine tenocytes were exposed to an siRNA targeting the transcription factor scleraxis (Scx) or a scramble control and maintained under cyclic strain. The resulting transcriptomes were then used for RNA-seq analysis. The goal of this study was to identify novel ways in which Scx facilitates mechanotransduction in tenocytes in order to better understand tenocyte biology.

2018-08-02 | GSE110567 | GEO

The transcription factor Scleraxis differentially regulates gene expression in tenocytes isolated at different developmental stages

Project description:Purpose:- RNA sequencing was performed on adult and fetal equine tenocytes expressing a specific short hairpin RNA against scleraxis (shSCX) versus a non-target (NT) scrambled control Methods:- mRNA profiles of four independent biological lines of adult and fetal NT and shSCX expressing tenocytes were generated by RNA sequencing, using Illumina NovaSeq6000. The sequence reads that passed quality filters were analyzed using the pseudoaligner Salmon and differential expression quantified using DESeq2. Gene ontology analysis was then conducted using Panther. Pathway analysis was conducted using GeneAnalytics. Network analysis was conducted using the STRING plugin in the Cytoscape app. Results:- SCX knockdown had a larger effect on gene expression in fetal tenocytes, effecting 477 genes in comparison to the 183 genes effected in adult tenocytes, indicating that SCX-dependent processes may differ in these two developmental stages.

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Transcriptional analysis of tenocytes from mice with a targeted deletion of scleraxis

Project description:We report RNA sequencing data from tenocytes cultured from the tail tendons of adult male mice in the C57Bl/6 background that either have the scleraxis gene (Scx+) or mice in which scleraxis has been deleted using CreERT2 driven from the Rosa26 locus using 4-hydroxytamoxifen (4HT).

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Expression data from embryonic day 15.5 atrioventricular canal regions were isolated from Scx-/- and Scx+/+ mice.

Project description:Purpose: Our lab has previously shown that Scleraxis (Scx) is require for proper valve development in vivo. In order to fully explore gene networks regulated by Scx during the vital stages of valve remodeling , high throughput RNA-squencing was performed. Results:There were a total of 18,810 genes were detected. A total of 864 genes were differentially expressed Scx null AVC regions: 645 being upregulated and 217 downregulated. In this data set, we include expression data from atrioventricular canal (AVC) regions from Scx null and wild-type littermate controls at embryonic day 15.5. A total of 6 samples were analyzed; 3 valve regions from E15.5 Scx-/- mice, and 3 from E15.5 Scx+/+ wild-type littermate controls. Differential expression read counts are ranked based on p-value (<0.05).

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Expression data from embryonic day 15.5 atrioventricular canal regions were isolated from Scx-/- and Scx+/+ mice.

2014-05-14 | GSE57423 | GEO

Transcriptional analysis of tendons from mice with a targeted deletion of scleraxis

Project description:We report RNA sequencing data from the plantaris tendons of adult male mice in the C57Bl/6 background that either have the scleraxis gene (Scx+) or mice in which scleraxis has been deleted using CreERT2 driven from the Rosa26 locus (Scx-). Mice in which scleraxis was deleted were created by crossing scleraxis-floxed mice with Rosa26-CreERT2 mice. Rosa26-CreERT2 mice that did not have a floxed scleraxis allele served as controls. Mice were treated with tamoxifen for 5 days to induce recombination at the scleraxis locus, and then subjected to a synergist ablation procedure in which the Achilles tendon is removed, resulting in compensatory growth of the plantaris tendon. Mice were analyzed either 7 or 14 days after synergist ablation. Control mice that did not undergo tamoxifen treatment or synergist ablation were also studied (NOC).

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Impact of exogenous IL-1ß stimulation on equine embryonic stem cell-derived tenocytes in three-dimensional culture

Project description:Exogenous IL-1ß stimulation impacts tendon-associated and inflammatory gene expression in equine adult tenocytes but has no impact on embryonic stem cell (ESC)-derived tenocytes in two-dimensional culture. Whether these effects translate to the transcriptome-wide level in three-dimensional (3D) culture in unknown. Utilising RNA-Sequencing, we report that ESC-tenocytes have zero differentially expressed genes following two-weeks of IL-1ß stimulation with similar collagen gel contraction values between the control and IL-1ß conditions, respectively.

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Genome-wide transcriptome analysis reveals Embryonic-Stem Cell derived tenocytes resemble fetal, not adult, tenocytes

Project description:Purpose:- RNA sequencing was performed on adult, fetal and embryonic stem-cell derived equine tenocytes cultured in 3D to look at which had more similar gene expression profiles. Results:- 6,190 genes were significantly differentially expressed (DE) across the three lines of fetal, adult and ESC-tenocytes (logFC ± 2, padj <0.01). 542 of these were DE between adult and fetal tenocytes, 2,708 between fetal and ESC-tenocytes and 2,940 between adult and ESC-tenocytes. Genes which were DE between adult and fetal tenocytes were significanlty involved in cell migration and motility. Genes which were DE between the ESC-tenocytes and both adult and fetal tenocytes were in organism process and development.

2020-05-28 | GSE145029 | GEO

Equine fetal, adult and embryonic stem cell derived tenocytes are all immune privileged but exhibit different immune suppressive properties in vitro

Project description:Purpose:- RNA sequencing was performed on adult, fetal and embryonic stem-cell derived equine tenocytes cultured in 2D to look at the difference in expression of genes associated with immune suppresion. Methods:- mRNA profiles of three independent lines of adult, fetal and ESC derived tenocytes were generated by RNA sequencing, using Illumina NovaSeq6000. The sequence reads that passed quality filters were analyzed using the pseudoaligner Salmon and differential expression quantified using DESeq2. Gene ontology analysis was then conducted using Panther GoSlim. Results:- 1691 genes were significantly upregulated in both fetal and adult tenocytes compared to ESC-tenocytes (logFC ± 2, padj <0.01). Response to stimulus and cell signalling were in the top 15 overrepresented pathways. The expression levels of 24 genes reportedly involved in MSC-mediated suppression of PBMCs were examined. 7 of these genes were more highly expressed in adult and/or fetal tenocytes compared to ESC-tenocytes, whereas 5 genes were expressed at lower levels in adult and/or fetal tenocytes than ESC-tenocytes.

2019-09-27 | GSE132358 | GEO

Transcriptional analysis of tenocytes from mice with a targeted deletion of scleraxis

Project description:Transcriptional analysis of tenocytes from mice with a targeted deletion of scleraxis

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