Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic profiling of synovial sarcoma transcriptome

ABSTRACT: We systematically explored the transcriptome of 10 synovial sarcoma (SS) patients. We detected a large number of upregulated and downregulated genes in SS compared to normal tissues, which were mainly involved in cell cycle, metabolic and P53 signaling pathways. Moreover, we identified a multitude of differentially alternative spliced genes, indicating that the deregulation of alternative splicing could be one of main factors contribute to the tumorigenesis of SS. A set of tumor-specific gene fusion pairs were identified in SS. We also detected dozens of differentially expressed circRNAs and their parental genes were enriched in muscle related biological process. The interaction network constructed based on circRNAs, miRNAs and corresponding target genes showed that the differentially expressed circRNAs in SS have the potential to regulate the expression of a number of SS related genes. Collectively, we systematically investigated the abnormal expression profile of SS and gain insights into the molecular mechanism from different views of transcriptome expression changes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE144190 | GEO | 2022/02/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Circular RNAs are a large class of animal RNAs with regulatory potency (RNA-Seq)

Project description:Circular RNAs (circRNAs) in animals are an enigmatic class of RNAs with unknown function. To systematically explore circRNAs, we sequenced and computationally analyzed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, with oftentimes tissue/developmental stage specific expression. Sequence analysis suggested important regulatory functions for circRNAs. Indeed, we discovered that human circRNA CDR1as is densely bound by miRNA effector complexes and harbors 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebra fish impaired midbrain development similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, indicating previously unrecognized regulatory potential of coding sequences. 1 Sample

2013-02-28 | E-GEOD-43572 | biostudies-arrayexpress

Circular RNAs are a large class of animal RNAs with regulatory potency (PAR-CLIP)

2013-02-28 | E-GEOD-43573 | biostudies-arrayexpress

The role of BFGF-related transcriptional regulation in calcification model of valve interstitial cells induced by osteoblastic medium

Project description:Purpose:To explore the the function and underlying mechanisms of basic fibroblast growth factor (BFGF) on calcific aortic valve disease (CAVD) a. Methods: The valvular interstitial cells were isolated from porcine aortic valve leaflets. To investigate the effect of BFGF on osteogenic differentiation of VICs, the osteogenic induced medium (OIM) and BFGF were added. RNA sequencing is used to identify changes in gene proffles. Results:This analysis completed the full transcriptome sequencing of 9 samples, with a total of 2 differentially expressed gene groups. The number of differentially expressed genes detected was 2526, 159. 6596 lncRNAs were identified, and the number of differentially expressed lncRNAs detected was 349,100. 6179 new circRNAs were predicted, and the number of differentially expressed circRNAs detected was 4,243. Conclusions:This study completed for the first time to the sequencing of the full transcriptome expression of valve interstitial cells under the action of BFGF, and has proved that BFGF can inhibit the calcification process of valve interstitial cells, our study suggests that bFGF has important value in the prevention and treatment of CAVD.

2023-05-01 | GSE225698 | GEO

CircTulp4 functions in Alzheimer’s disease pathogenesis by regulating its parental gene Tulp4

Project description:Here, we systematically investigated circRNAs in the APP/PS1 model mouse brain through deep RNA-sequencing. We report that circRNAs are markedly enriched in the brain and that several circRNAs exhibit differential expression between wild-type and APP/PS1 mice. We characterized one abundant circRNA, circTulp4, derived from Intron1 of the gene Tulp4. To investigate the effect of CircTulp4 on chromatin status, we used ATAC-seq to investigate the chromatin accessibility upon CircTulp4 knockdown.

2021-02-28 | E-MTAB-9919 | biostudies-arrayexpress

CD54–NOTCH1 axis controls tumor initiation and cancer stem cell functions in human prostate cancer

Project description:Using high sensitive ArrayStar Human, we detected differentially expressed genes and circRNAs, these part of data is the aberrent expressed genes.

2016-04-13 | GSE80209 | GEO

MicroRNAomes of cattle intestinal tissues revealed possible miRNA regulated mechanisms involved in Escherichia coli O157 fecal shedding

Project description:The current study aimed to investigate whether bovine non-coding RNA play a role in regulating E. coli O157 shedding through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 to 413 ± 49. Compared between SS and NS, the number of differentially expressed (DE) miRNAs ranged from one to eight, and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (8 and 7, respectively). Functional analysis indicated that the bta-miR-378b, bta-miR-2284j and bta-miR-2284d which were down-regulated in both distal jejunum and rectum of SS, the bta-miR-2887 which was down-regulated in rectum of SS, as well as the bta-miR-211 and bta-miR-29d-3p which were up-regulated in rectum of SS were potentially regulatory to host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that the alternation of miRNA expression in the gut of SS may lead to differential regulation in immune functions involved in E. coli O157 super-shedding in cattle.

2018-10-30 | GSE121916 | GEO

MicroRNAomes of cattle intestinal tissues revealed possible miRNA regulated mechanisms involved in Escherichia coli O157 fecal shedding

2018-12-01 | GSE96973 | GEO

Transcriptomic Analysis in Renal T Lymphocytes Exposes Sodium-Independent Dietary Differences in Dahl Salt-Sensitive Rats

Project description:Background. The Dahl salt-sensitive (SS) rat is an established model of salt-sensitive hypertension and renal damage. Recently, sodium-independent dietary effects were shown to be important in the development of the SS hypertensive phenotype. Compared to Dahl SS/JrHsdMcwi (SS/MCW) rats fed a purified diet (AIN-76A), grain-fed Dahl SS/JrHsdMcwiCrl rats (SS/CRL; Teklad 5L2F) were less susceptible to salt-induced hypertension and renal damage. Methods. With the known role of the immune system in hypertension, the present study characterized the immune cells infiltrating SS/MCW and SS/CRL kidneys. To further identify distinct molecular pathways between SS/MCW and SS/CRL, transcriptomic analysis was performed via RNA sequencing in T-cells isolated from the blood and kidneys of low and high salt-fed rats. Results. Following a 3-week high salt (4.0% NaCl) challenge, SS/CRL rats were protected from salt-induced hypertension (116.5±1.2 vs 141.9±14.4 mmHg) and albuminuria (21.7±3.5 vs 162.9±22.2 mg/day) compared to SS/MCW. Additionally, the absolute number of immune cells infiltrating the kidney was significantly reduced in SS/CRL. RNA-seq revealed >50% of all annotated genes in the entire transcriptome to be significantly differentially expressed in T-cells isolated from blood versus kidney. Pathway analysis of significant differentially expressed genes between SS/MCW and SS/CRL renal and circulating T-cells demonstrated salt-induced changes in genes related to inflammation in SS/MCW compared to metabolism-related pathways in SS/CRL. Conclusions. These functional and transcriptomic T-cell differences between SS/MCW and SS/CRL show that sodium-independent dietary effects may influence the immune response and infiltration of immune cells into the kidney, ultimately impacting susceptibility to salt-induced hypertension and renal damage.

2019-08-26 | GSE127000 | GEO

Circular RNAs expression profiles in human gastric cancer

Project description:The circRNAs expression profiles in 5 gastric cancer (GC) and their matched non-gastric cancer (non-GC) tissues were detected by human circRNA expression profile chips, and the differentially expression circRNAs between GC and matched non-GC tissues were then identified. A total of 713 circRNAs were differentially expressed in GC tissues vs. non-GC tissues (fold change≥2.0, p<0.05) among all the candidate circRNAs (62998) detected in both GC and non-GC tissues according to the T-test. 191/713 circRNAs were significantly upregulated in GC tissues, whereas 522/713 circRNAs were significantly downregulated in GC tissues. GO and KEGG pathway analyses showed that many dysregulated circRNAs may be functionally GC-related, thereby contributing to the development of GC.

2017-06-19 | GSE100170 | GEO

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed

Project description:Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers. To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).

2015-04-24 | E-GEOD-65926 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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