Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hepatic miRNA expression in experimental biliary atresia

ABSTRACT: Hepatic microRNA was measured by Exiqon array in the mouse RRV model of biliary atresia miRNA expression profiling. For the miRNA microarray experiment, RRV and saline injected animals were euthanized at 3, 8, and 14 days post infection (n=5 per treatment, per time point), and total RNA was purified from liver using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. A pooled common control was assembled from an equal RNA mass from each of the samples, and samples and control were separately dye-labeled, and hybridized to a miRcury v11.0 miRNA microarray (Exiqon) at the University of Pennsylvania School of Medicine Microarray core facility. Sample hybridization intensities were scored relative to the common control, and raw intensity data were normalized and analyzed using the SAM add-in for Microsoft Excel. MiRNAs exhibiting a fold-change of greater than 10% up or down, at a false discovery rate of 5% were chosen for further study. Three time points (3, 8, 14 days) x 2 conditions x 6 replicates - 1 failed sample = 35 samples

ORGANISM(S): Mus musculus

SUBMITTER: Joshua Friedman

PROVIDER: E-GEOD-33418 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Exiqon]

Project description:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line (control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed. 189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates. 3045 target genes in total were detected with 587 common and 2458 unique target genes between up and downregulated miRNAs.The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis. Comparison in triplicates the miRNA expression profile with Exiqon between human JJ012 chondrosarcoma cell line and C28 control chondrocytes

2013-08-28 | E-GEOD-48396 | biostudies-arrayexpress

miRNA and consolidation of cued fear memory

Project description:miRNA profiling was carried out using the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno) miRNA were profiled in amygdala brain tissue obtained from adult mice 30 mins after auditory fear conditioning and expression levels compared to tissue obtained from Home cage controls Adult male mice were fear conditioned using tone-shock pairings and brains were harvested 30 mins later. The brains of Home Cage controls and Fear Conditioned animals (n = 4/group) were then punched to collect amygdala tissue. miRNA were extracted using the Qiagen miRNeasy Kit, and then shipped to Exiqon. Exiqon performed labeling, hybridization and data analysis after use of the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno). https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Array-6th-gen-hsa-mmu-rno-manual.pdf

2014-09-30 | E-GEOD-59072 | biostudies-arrayexpress

MicroRNA response to Snail overexpression in lung cancer cell lines

Project description:Analysis of four lung cancer cell lines transfected with a vector expressing the transcriptional repressor Snail versus a vector control. Aberrant Snail expression is known to induce an EMT program in lung cancers. Four lung cancer cell lines (H292, H358, H441, H1437) with stable overexpression of the human SNAI1 gene and vector expressing controls were collected at equal confluency with the miRNeasy Mini kit (Qiagen). One microgram of total RNA was labeled using miRCURY LNA™ microRNA Array Power Labeling kit by the UCLA Clinical Microarray Core. The labeled miRNAs were hybridized to Exiqon miRCURY LNA microRNA Array-6th Generation according to the manufacturer’s instructions. This array includes 927/648/351 human/mouse/rat miRNAs as well as 438 miRPlus miRNAs. The miRNA array slides were scanned using Axon GenePix 4000B scanner (Axon Instruments, Foster City, CA) and processed by using the GenePix Pro 6.0 software (Axon Instruments). The raw data were normalized by using a combination of housekeeping miRNA, spike-in miRNA and invariant endogenous miRNAs.

2013-07-17 | E-GEOD-48922 | biostudies-arrayexpress

MicroRNA Expression in Kidney Development Comparing E14.5 and P1

Project description:This study was performed to identify miRNAs that are differentially regulated during mouse kidney development. Two stages (E14.5 and P1) were analyzed. Differential expression was verified using qPCR and/or in situ hybridization. Multiple kidneys were dissected, pooled and processed for total mRNA isolation. Probe labeling, hybridization and data analysis were performed by Exiqon. The three submitted sample files are technical replicas using the same mRNAs.

2010-06-20 | E-GEOD-18609 | biostudies-arrayexpress

miRNA profiling in high-grade serous ovarian carcinoma

Project description:In this study, we performed miRNA profiles analysis of high-grade serous ovarian carcinoma compared to normal fallopian tube fimbria using microarray (Exiqon, Denmark) to evaluate their potential role in the pathogenesis of uterine leiomyoma. miRNA profiling analysis of the 10 samples including 5 high-grade serous ovarian carcinomas and 5 normal fallopian tube fimbria.

2014-11-14 | E-GEOD-61485 | biostudies-arrayexpress

Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples

Project description:Baseline microRNA (miRNA) expression was evaluated in 107 HapMap lymphoblastoid cell lines (LCLs; 53 CEU and 54 YRI) using Exiqon miRCURY LNA arrays v10.0 (Exiqon array). Total RNA from each of the 107 HapMap sample was labeled and hybridized onto an Exiqon array

2012-07-28 | E-GEOD-34406 | biostudies-arrayexpress

Regulation of onco and tumor suppressor miRNA by mTORC1 inhibitor PRP-1 in human chondrosarcoma

Project description:The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 not treated (Control) and JJ012 chondrosarcoma cell line treated with antitumorigenic neuropeptide PRP-1. The goal was to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays,was performed. performed.211 unique gene targets were detected for downregulated miRNAs and 104 unique target genes for upregulated miRNAs with 28 target genes common for both. out of 122 upregulated and 109 downregulated , total 9 differentially statistically significant miRNAs(3 upregulated and 6 downregulated) fitting P<0.05 by Benjamini Hochberg were detected when comparing chondrosarcoma cell line treted to not treated control using human Exiqon arrays with biological triplicates.: miR192, regulating cell cycle checkpoinrts was upregulated in treated samples 4 fold, miR125b, known as tumor suppressor in sarcomas was upregulated 4.87 fold. miR20a was upregulated 5.29 , known to form complexes with Argonaute proteins-part of RNA induced silencing complex (RISC) Downregulated miRNas included miR509-3p (12.88 fold), its targets Yap, Rac1 and Yes1 known to be associated with Src kinase activity; miR589 was downregulated 7.46 fold , targets Src adaptors'. miR 302c was downregulated6.46 fold and miR199a=5p -5.66 fold , that acted as oncogenes in sarcomas. miR584 involved on cell migration and TGFbeta signaling was downregulated 4.78 fold Comparison of miRNA expression between control samples and samples treated with antiproliferative cytostatic mTORC1 inhibitor PRP-1 cytokine in human chondrosarcoma JJ012 cell line

2013-10-31 | E-GEOD-49545 | biostudies-arrayexpress

Profiling of circulating microRNAs in patients with Barrettâ??s esophagus and esophageal adenocarcinoma

Project description:miRNAs were extracted from plasma samples of healthy volunteers, patients with Barrettâ??s esophagus and patients with esophageal adenocarcinoma. We used the Serum / Plasma Focus miRNA PCR panel (Exiqon, Denmark) to quantitate miRNA presence in the different patient groups. PCR miRNA profiling. miRNA from three different patient groups were extracted from their plasma.

2015-11-19 | E-GEOD-51410 | biostudies-arrayexpress

M2 cytokines alter the miRNA expression profile in macrophages

Project description:To examine the miRNA expression profile of the profibrogenic macrophages, we compared miRNA expression in untreated versus IL-4 or IL-13-treated macrophages using miRNA microarray.IL-4 and IL-13 treatment resulted in marked changes in 18 and 19 miRNAs in macrophages, respectively.(n=3, fold changes>2, P<0.05) Total RNA from human primary macrophages (n=3) treated with or without 20 ng/ml IL-4 or 20ng/ml IL-13 for 48 hr was isolated with a mirVana miRNA Isolation kit (Ambion, Foster, CA). The miRNA expression profile of the samples were examined using miRCURY LNAM-bM-^DM-" arrays (v18.0; covering 1921 human miRNAs, Exiqon ,Vedbaek, Denmark).

2014-07-12 | E-GEOD-59348 | biostudies-arrayexpress

Human HPV16 positive CaSki cells: Control vs. virus oncogene e6/e7 silenced

Project description:The infection with high-risk human papillomavirus is aetiologically linked to cervical cancer, the role of miRNAs regulated by virus oncogene in cancer progression remain largely unknown. Here, we screened the differentially expressed miRNAs with miRNA array between virus oncogene e6/e7 silenced and not in HPV16-positive cervical cancer cell lines In the study, we screened the differentially expressed miRNAs with miRNA array (Exiqon, miRCURY LNA microRNA array, 7th gen [hsa, miRBase 18]) between virus oncogene e6/e7 silenced and not in HPV16-positive cervical cancer cell lines to found miRNAs regulated by virus oncogene e6/e7. Biological replicates: 3 control, 3 e6/e7 silenced, independently grown and harvested. four replicates per array.

2016-07-01 | E-GEOD-68153 | 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