Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discovery of novel microRNAs in rat kidney using microarray analyses

ABSTRACT: MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs. Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys.

ORGANISM(S): Mus musculus Rhinopithecus bieti Pan troglodytes Canis lupus familiaris Saguinus labiatus Ateles geoffroyi Ovis aries Macaca nemestrina Petromyzon marinus Xenopus laevis Symphalangus syndactylus Oryzias latipes Bos taurus Rattus norvegicus Takifugu rubripes Pan paniscus Homo sapiens Pongo pygmaeus Xenopus tropicalis Danio rerio Equus caballus Sus scrofa Gallus gallus Tetraodon nigroviridis Taeniopygia guttata Ornithorhynchus anatinus Macaca mulatta

PROVIDER: GSE33360 | GEO | 2011/11/02

SECONDARY ACCESSION(S): PRJNA149019

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Discovery of novel microRNAs in rat kidney using microarray analyses

Project description:MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs. Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys. Four male, 6-week-old Big Blue rats were treated with 10.0 mg/kg aristolochic acid(AA) 5 times a week for 12 weeks, four untreated rats as control. The animals were sacrificed 1 day after the last treatment and total RNA were isolated. All eight rat samples were used to deep sequencing analyses (University of Texas Southwestern Medical Center Microarray Core Facility), while 6 samples (3 AA-treated and 3 control) were used to custom vertebrate microRNA microarray analysis (LC Sciences). We used the miRanalyzer standalone version for the prediction of novel microRNAs and microRNA microarray to confirm novel microRNAs.

2011-11-02 | E-GEOD-33360 | biostudies-arrayexpress

Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer

Project description:In order to improve our understanding of breast cancer (BC) biology and its prognostication, global miRNA expression profiling was performed using microarray technology on systemically untreated BC patients with long-term follow up. In this study, global miRNA expression profiling using microarray technology was conducted on 56 systemically untreated BC patients with long-term follow up. The arrays used for miRNAs expression profiling comprise a total of 640 probes targeting 328 human miRNAs (hsa-miRs), as well as mouse and rat miRNAs, from the miRBase Sequence Database version 8.0.

2011-07-01 | E-GEOD-28321 | biostudies-arrayexpress

Micronome profiling in 3 pairs of salivary adenoid cystic carcinoma(SACC) and the corresponding nomal salivary gland tissues

Project description:To screen miRNAs for potential NDRG2 regulation, we performed micronome profiling in 3 pairs of SACC samples and the corresponding normal salivary glands. The sequencing analysis generated approximately 1,000,000 clean reads per sample. All reads were mapped to annotated miRNAs in the miRBase database (version 22), whereas approximately 45% of the clean reads were mapped to mature miRNAs in the database. After applying a stringent filtering criterion to compare the results from SACC tumor tissue and the adjacent normal salivary glands (log2 fold change >1, FDR<0.05), we identified 176 dysregulated miRNAs.

2018-12-25 | GSE117275 | GEO

miRNA expression-based, individualized outcome prediction for SDT treatment in melanoma

2015-01-29 | GSE65390 | GEO

Differentially expressed miRNA in burned murine skin tissue compared to normal skin tissue

Project description:Interactions between stromal cell-derived factor-1M-NM-1 (SDF-1M-NM-1) and its cognate receptor CXCR4 are crucial for the recruitment of mesenchymal stem cells (MSCs) from bone marrow (BM) reservoirs to damaged tissues for repair during alarm situations. MicroRNAs are differentially expressed in stem cell niches, suggesting a specialized role in stem cell regulation. Here, we gain insight into the molecular mechanisms involved in regulating SDF-1M-NM-1. Individualized outcome prediction classifiers were successfully constructed through expression profiling of microRNAs (in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk))in one burned murine skin tissue compared to normal skin tissue,which had 57 upregulated microRNAs and 28 down-regulated microRNAs. In the study presented here, a consecutively operated, well-defined cohort of 2 cases, was used to acquire expression profiles of microRNAs (in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk)), leading to the successful construction of supervised. The most recent version of the array (v.11.0 - hsa, mmu & rno array) contains more than 1700 capture probes, covering all microRNAs annotated in miRBase 11.0, as well as all viral microRNAs, related to these species.

2013-05-02 | E-GEOD-46558 | biostudies-arrayexpress

miRNA expression-based, individualized outcome prediction for SDT treatment in melanoma

Project description:Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 3100 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 18.0, in 8 melanoma samples divided into 4 groups (Control, ALA, US, and SDT group). In the study presented here, a consecutively operated, well-defined cohort of 8 melanoma cases was used to acquire miRNA expression profiles with Exiqon arrays based on miRBase 18.0.

2015-01-29 | E-GEOD-65390 | biostudies-arrayexpress

Evaluation of quantitative miRNA gene expression platforms - custom microRNA GeneChip

Project description:MicroRNA microarray expression dataset used to develop novel and robust quality metrics to objectively assess platform performance of very different technologies. The HsMir v1s520779F custom array is primarly based on the commercially available Affymetrix microRNA microarray version 2.0 (Affymetrix GeneChip miRNA 2.0 Array datasheet P/N EXP00180 Rev 1) with i) microRNA probe sequences updated using miRBase version 17 ii) all human pre-microRNAs removed iii) all non-human sequences removed iv) all viral target sequences removed. In summary, the array contains 1738 mature microRNAs and 2333 other small RNAs (such as small nucleolar RNAs or small cajal body-specific RNAs) probe sequences plus the Affymetrix hybridization and normalization control probesets.

2013-08-09 | E-GEOD-49661 | biostudies-arrayexpress

Differential microRNA expressions during development of mouse cornea

Project description:Expression of microRNAs (miRNA) was examined in the wild type mouse cornea at postnatal day 9 (PN9) before stratification of the corneal epithelium and at 6 weeks of age when the epithelium is fully stratified. Using Sanger miRBase Version 10.0, we analysed 568 miRNAs across 4 biological replicates of the developing (PN9) and mature (6-week-old) mouse cornea.

2010-05-16 | E-GEOD-16396 | biostudies-arrayexpress

MicroRNA expression in rat soleus muscle during atrophy induced by hindlimb suspension

Project description:The objective of the study was to identify microRNAs expressed in the rat soleus muscle and determine if their expression was changed in response to hindlimb suspension. The microRNA expression profile (Sanger miRBase 9.0) of the rat soleus muscle was determined in the following three groups: control (C), hindlimb suspended for 2 days (HS-2) or 7 days (HS-7). Three replicates were performed for each group.

2009-08-25 | E-GEOD-17776 | biostudies-arrayexpress

Transcription profiling of hearts and kidneys of spontaneously hypertensive rat and coisogenic rat strain with connexin50 mutation

Project description:We aimed to compare transcriptome in heart and livers of spontaneously hypertensive rat SHR/OlaIpcv (Rat Genome Database ID: 631848) versus coisogenic rat strain SHR-Gja8m1Cub (Rat Genome Database ID: 2293729) using Affymetrix GeneChipÂ® Rat Exon 1.0 ST Arrays in triplicate. Affymetrix GeneChipÂ® Rat Exon 1.0 ST Array was used to determine the transcriptomic characteristics of the SHR and the coisogenic strain SHR-Dca. We extracted total RNA from the kidneys and hearts of 4-month old males of both strains using phenol-chloroform and purified with the RNeasy Mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturerâs protocol. The quality of the total RNA was verified by the Agilent 2100 Bioanalyzer system. Double-stranded complementary DNA (cDNA) was synthesized from total RNA. The labeled and fragmented cDNA was pooled for each strain (SHR, SHR-Dca) and tissue (heart, kidney) and hybridized to Affymetrix GeneChipÂ® Rat Exon 1.0 ST Arrays in triplicate (total 12 arrays). The whole hybridization procedure including DNA adjustment was performed according to the protocol recommended by Affymetrix.

2016-07-01 | E-MTAB-4542 | 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