Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Circular RNA sequencing of four cell lines

PROVIDER: PRJNA504519 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8173610_1.fastq.gz	Fastqsanger.gz
	SRR8173610_2.fastq.gz	Fastqsanger.gz
	SRR8173607_1.fastq.gz	Fastqsanger.gz
	SRR8173607_2.fastq.gz	Fastqsanger.gz
	SRR8173608_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Enzyme-free digital counting of endogenous circular RNA molecules in Formalin-Fixed Paraffin-Embedded tissues from patients with B-cell malignancies

Project description:Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies. We quantified circular RNA expression by total RNA sequencing of four different Mantle Cell Lymphoma cell lines, REC-1, Granta-519, Z138 and UPN2 and the Multiple Myeloma cell line, H929.

2017-12-15 | GSE108111 | GEO

DOCK1 gene derived hsa_circ_0020397 RNA is over-expressed in luminal mammary tumors and it is involved in the epithelial differentiation, growth and motility of the neoplastic cell

Project description:Circular-RNAs are an emerging group of regulatory molecules involved in the control of numerous cellular processes and may play a role in the growth and diffusion of various types of tumors. In the present study, we define the expression of 15 selected circular-RNAs, which may be involved in the process of epithelial-to-mesenchymal-transition, using a panel of 18 breast cancer cell-lines recapitulating the heterogeneity of the tumor and consisting of three distinct groups according to the mesenchymal/epithelial phenotype. The circular RNA deriving from the DOCK1 gene (hsa_circ_0020397) is characterized by the most interesting expression profile, as it is undetectable in triple-negative mesenchymal cell-lines, while it is easily measurable in epithelial cell-lines independent of their positivity to estrogen receptor or the HER2 membrane receptor. Whole-genome RNA-sequencing experiments performed on the triple-negative/mesenchymal MDA-MB-231 and MDA-MB-157 cell-lines engineered to over-express hsa_circ_0020397 demonstrate that the circular-RNA controls the expression of 110 common genes. Pathway analysis of these genes indicate that over-expression of the circular-RNA differentiates the two mesenchymal cell-lines along the epithelial pathway and increase cell-to-cell adhesion. This is accompanied by a growth inhibitory effect and a reduction in the random/directional motility of the two cell-lines. The up-regulated AGR2, ENPP1 and PPP1R9A genes as well as the down-regulated APOE, AQP3, CD99L2 and IGFBP4 genes show an opposite regulation by circDOCK1 silencing in CAMA1 luminal cells.

2022-06-15 | E-MTAB-10819 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Diabetic db/db Mice Islets Transcriptomes

Project description:Circular RNAs constitute an extensive fraction of the mammalian transcriptome.In this study, circular RNAs dysregulated in the islets of diabetic db/db mice were identified by high-throughput RNA sequencing. More than 5000 circRNAs were detected using RNA sequencing, indicating that circular transcripts were abundant in islets. Among them, we found that circ-Tulp4 showed significant downregulation in diabetic mouse islet cells. Further experiments indicated that modulating the expression of circ-Tulp4 in β cell lines desensitized β-cells to lipotoxicity.

2020-10-28 | GSE138096 | GEO

Investigating the circular RNA gene expression characteristics in salivary adenoid cystic carcinoma (SACC) cells

Project description:To further investigate the circular RNA gene expression characteristics in SACC cell lines, we utilized the SBC Human (4*180K) ceRNA microarray to identify differential circular RNAs between SACC-83 and SACC-LM cells.

2024-04-18 | GSE263719 | GEO

The profile of circular RNA in lung cancer cell lines

Project description:Circular RNA is found to play a part in lung cancer progreession. The aim of our study is trying to identify a key circular RNA expression profile by using numerous lung cancer cell lines. Hopefully, the results from our study could be a relevant biomarker in the clinic.

2021-12-31 | GSE183375 | GEO

Intronic Circular RNA hsa_circ_0092339 Plays as Molecular Sponge in Castration-resistance Prostate Cancer by hsa-mir-940/C-MYC Axis

Project description:Generally, only exonic circular RNA is believed to play the role as molecular sponge, while the main function of intronic circular RNA is regulating the expression of its parental gene. We aimed to find out whether intronic circular RNA could also act as molecular sponge in castration-resistance prostate cancer. Gene chip of castration-resistant and hormone-sensitive prostate cancer cell lines was sequenced to identify the differentially expressed circular RNA. We demonstrated that intronic circular RNA hsa_circ_0092339, located in the nucleus, was highly expressed in castration-resistance prostate cancer (CRPC) cell lines by using high throughput RNA sequencing. By knocking down hsa_circ_0092339, we found that this intronic circular RNA did not regulate the expression of its parental gene. By RIP and RNA pull-down experiment, we further found hsa_circ_0092339 realized its function by acting as molecular sponge. Hsa_circ_0092339 prevented degradation of C-MYC by absorbing hsa-mir-940 and preventing it enter the cytoplasm from nucleus. The combination of hsa-mir-940 and C-MYC was certified by dual-luciferase assay. In addition, we proved this axis was also effective in CRPC xenografted model. The effectiveness of this pathway in tissues was verified by animal experiments.

2023-01-01 | GSE185910 | GEO

Circular RNAs in nasopharyngeal carcinoma cell lines with different metastasis potential

Project description:Increasing evidence has demonstrated a significant role for circular RNAs (circRNAs) in tumorigenesis. However, their functions in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, a model compared high and low metastatic NPC cell lines (S18 vs. S26) was constructed to determine the expression profile of circRNAs using the RNA sequencing analysis.

2020-02-24 | GSE137543 | GEO

The profile of circular RNA in lung cancer cell lines

Project description:The profile of circular RNA in lung cancer cell lines

| PRJNA760444 | ENA

Analyzing ceRNA networks involved in KSHV lytic replication mediated by vIRF1 or vFLIP.

Project description:Whole-transcriptome sequencing (RNA sequencing [RNA-seq]) was performed in the viral producer cell lines iSLK-RGB BAC16,iSLK-RGB-K9 mutant and iSLK-RGB-K13 mutant cells to uncover the global landscape of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), mRNAs and microRNAs (miRNAs) in KSHV replication mediated by vIRF1 or vFLIP.

2022-02-24 | GSE180921 | GEO

Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

Project description:Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues. Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins. Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons. The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis. In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function. Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing

2015-02-25 | E-GEOD-61991 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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