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Multiple tissue sequencing of WT and Scx-ko mice

ABSTRACT: We used RNA sequencing and a gene knockout mice model to reveal the critical functions of Scx in multiple tissues.

ORGANISM(S): Mus musculus

PROVIDER: GSE139025 | GEO | 2022/10/14

REPOSITORIES: GEO

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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).

2014-05-14 | E-GEOD-57423 | biostudies-arrayexpress

RNA Sequencing Facilitates Quantitative Analysis of Cont/Dicer KO/Scx HT mice Achilles Tendon Transcriptome

Project description:To investigate which mRNA and miRNA are involved in Dicer KO mouse tendon hypoplasticity, we performed RNA-seq and small RNA-seq using RNA from Achilles tendon of Cont (Dicer f/f), Scx HT (ScxCre/+ Knock In:Dicer +/+) and Dicer KO (ScxCre/+ Knock In:Dicer f/f) mice at 4 weeks of age. Achilles tendon from 4-week-old female mice was harvested, RNA was isolated using an RNA extraction kit. RNA libraries were generated and sequenced by K. K. DNAFORM (Tokyo, Japan). The libraries were sequenced by Illumina HISEQ4000 using Illumina provided protocol. Differential gene expression was analyzed with R Bioconductor DESeq2. We found that a large portion of tendon-fibroblast characteristic genes was downregulated in Dicer KO mice Achilles tendon compared to Cont and Scx HT.

2022-05-31 | GSE186353 | GEO

Single cell RNA-seq of limb cells from E12.5 WT and Scx-ko mice

Project description:We used single-cell RNA sequencing and a gene knockout mice model to reveal the heterogeneity and differentiation trajectory of embryonic limb cell in both physiological and pathoplogical conditons.

2022-10-14 | GSE138929 | GEO

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

2014-05-14 | GSE57423 | GEO

Genome-wide identification of Scx transcriptional target genes in tendon development II

Project description:Despite their important roles in the musculoskeletal system, tendon and ligaments are much less studied comparing to bone, cartilage and muscle. The lack of knowledge in tendon biology severely hinders the understanding of the etiologies of tendon related diseases and development of efficient clinical treatments. In mouse, Scx gene, encoding a Twist family bHLH transcription factor, is expressed in progenitors of all tendons and ligaments, as well as in mature tenocytes. Previous studies show that inactivation of Scx gene results in absence or severe hypoplastia of force transmitting tendons, with muscle anchoring tendons and ligaments are less affected. Here we report a set of ChIPseq data from E13.5 forelimbs of novel Scx-2xFlag tagged mice in which a Scx-Flag fusion protein is expressed recapitulating endogenous Scx expression, and a set of RNAseq data of Scx-GFP positive cells from E13.5 Scx wildtype, E15.5 Scx wildtype and homozygous mutant forelimbs. Using RNAseq and ChIPseq assays, we identify several genes exhibiting Scx-dependent tendon expression druing differentiation, with Scx binding peaks located within their promoter/enhancer regions. Thus these genes may play critical roles in mediating Scx regulated tendon cell differentiation. Our results provide new insights in the mechanisms of tendon development.

2021-06-28 | GSE173428 | GEO

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

Liver Circadian RNA-Seq from WT and Bmal1 muscle-specific KO (mKO) mice

Project description:Transcriptomic analysis to reveal the impact of muscle-specific Bmal1 knockout on daily cycles of gene expression in the liver

2023-04-05 | GSE171432 | GEO

RNA-seq analysis of Scx-lineage cell depletion to investigate tendon cell functions during flexor tendon healing

Project description:Little is understood about the roles of tendon cells during flexor tendon healing. To better understand tendon cell functions, the Scx-Cre mouse was crossed to the DTR mouse model to facilitate scleraxis lineage cell depletion prior to acute flexor tendon injury and repair. WT (cre-) and experimental (cre+) mice underwent complete transection and repair of the flexor digitorum longus tendon. Repaired tendons were harvested at 14 and 28 days post-repair for bulk RNA-Seq analysis to examine possible mechanisms driving differential healing due to Scx lineage cell depletion.

2021-02-08 | GSE156157 | GEO

RNA-sequencing of liver from WT and CRY1 KO mice

Project description:We conducted RNA-sequencing from three per group C57BL/6J male mice, ten weeks old. Liver tissue was collected from wild-type (WT) and Cryptochrome1 (CRY1) knockout (KO) mice.

2022-08-16 | GSE197839 | GEO

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

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

| PRJNA433994 | ENA

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