Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterisation of dysplastic liver nodules using low-pass sequencing and the proof of principle on liquid biopsies

ABSTRACT: Characterisation of dysplastic liver nodules using low-pass sequencing and the proof of principle on liquid biopsies

PROVIDER: PRJEB20592 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1950870.fastq.gz	Fastqsanger.gz
	ERR1950880.fastq.gz	Fastqsanger.gz
	ERR1950890.fastq.gz	Fastqsanger.gz
	ERR1950900_1.fastq.gz	Fastqsanger.gz
	ERR1950900_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 405

Similar Datasets

P. vivax: proof-of-principle global transcription analysis from two wild isolates

Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. To determine the extent of cross-hybridization of P. falciparum with P. vivax, and to determine overlaps in expression profiles of the P. vivax Sal1 monkey-adapted strain vs wild isolates, single dual hybridization analyses were performed.

2008-04-12 | E-GEOD-11075 | biostudies-arrayexpress

Pre-clinical proof of principle for orally delivered Th17 antagonist miniproteins

Project description:Pre-clinical proof of principle for orally delivered Th17 antagonist miniproteins

| PRJNA1096346 | ENA

P. vivax: proof-of-principle global transcription analysis from two wild isolates

2008-04-12 | GSE11075 | GEO

P. vivax: proof-of-principle global transcription analysis from two wild isolates

Project description:P. vivax: proof-of-principle global transcription analysis from two wild isolates

| PRJNA107065 | ENA

Proof of principle for iPS2-10X-seq: timecourse experiment during 2D cardiac differentiation

Project description:Proof of principle for iPS2-10X-seq: timecourse experiment during 2D cardiac differentiation

| PRJEB75579 | ENA

Proof of principle for iPS2-10X-seq: cardioids experiment during 3D cardiac differentiation

Project description:Proof of principle for iPS2-10X-seq: cardioids experiment during 3D cardiac differentiation

| PRJEB75583 | ENA

Project description:ChAMP proof of principle

| PRJNA1041053 | ENA

Specific patterns of PIWI-interacting small noncoding RNA expression changes in dysplastic liver nodules and hepatocellular carcinoma

Project description:Hepatocellular carcinoma (HCC) is considered the result of a stepwise carcinogenic process, more often beginning with development of premalignant lesions within a cirrhotic liver, morphologically characterized by low- (LGDN) and high-grade (HGDN) dysplastic nodules. Piwi-interacting RNAs (piRNAs) represent a large family of small noncoding (snc) RNAs, 23-35 nucleotide-long, first identified in fruitfly germline cells by their ability to interact with PIWI proteins and thereby exert epigenetic and post-transcriptional regulation of gene expression. The PIWI-piRNAs pathway is active also in human somatic tissues, including stem and cancer cells, where piRNAs and piRNA-like molecules have been shown to influence key cellular processes. We applied small RNA sequencing to search for human liver piRNAs and to profile their expression patterns in cirrhotic nodules (CNs), LGDN, HGDN, early HCC (eHCC) and progressed HCC (pHCC), aiming at identifying possible relationships between these sncRNAs and liver carcinogenesis. Analyzing 54 nodules (14 CN, 8 LGDN, 6 HGDN, 6 eHCC and 20 pHCC) from 17 patients, we identified a 125 piRNA expression signature that clearly discriminates HCC from matched CNs, correlating also to clinicopathological characteristics of HCC. This result was confirmed by functional analysis of predicted piRNA target mRNAs. Interestingly, 24 piRNAs showed specific expression patterns in dysplastic nodules, respect to cirrhotic liver and/or pHCC. These results demonstrate that the piRNA pathway is active in human liver, where it is likely to represent a new player in the molecular events that characterize hepatocellular carcinogenesis, from early stages to pHCC. Furthermore, they suggest that piRNAs might represent new disease biomarkers, potentially useful for differential diagnosis of dysplastic and neoplastic liver lesions.

2016-07-15 | E-MTAB-3973 | biostudies-arrayexpress

A new strategy for identifying mechanisms of drug-drug interaction using transcriptome analysis: Compound Kushen injection as a proof of principle

Project description:Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. We generated and analysed transcriptome data from cells treated with single treatments or combined treatments and our analysis showed that opposite directions of regulation for pathways related to DNA synthesis and metabolism appeared to be the main reason for different effects of CKI when used in combination with chemotherapy drugs . We also found that pathways related to organic biosynthetic and metabolic processes might be potential targets for CKI when interacting with doxorubicin and 5-Fu. Through co-expression analysis correlated with phenotype results, we selected the MYD88 gene as a candidate major regulator for validation as a proof of concept for our approach. Inhibition of MYD88 reduced antagonistic cytotoxic effects between CKI and 5-Fu, indicating that MYD88 is an important gene in the DDI mechanism between CKI and chemotherapy drugs. These findings demonstrate that our pipeline is effective for the application of transcriptome analysis to the study of DDIs in order to identify candidate mechanisms and potential targets.

2019-08-20 | GSE130359 | GEO

Single-cell mitochondrial mutation lineage tracing of non-dysplastic and dysplastic Barrett's esophagus

Project description:Single-cell mitochondrial mutation lineage tracing of non-dysplastic and dysplastic Barrett's esophagus

| PRJNA1231604 | ENA