Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA-Seq identifies a serum miRNA panel which can detect and monitor liver disease in pediatric cystic fibrosis

ABSTRACT: miRNA-Seq identifies a serum miRNA panel which can detect and monitor liver disease in pediatric cystic fibrosis

PROVIDER: PRJNA438068 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6829190.fastq.gz	Fastqsanger.gz
	SRR6829191.fastq.gz	Fastqsanger.gz
	SRR6829192.fastq.gz	Fastqsanger.gz
	SRR6829193.fastq.gz	Fastqsanger.gz
	SRR6829194.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

miRNA-Seq identifies a serum miRNA panel which can detect and monitor liver disease in pediatric cystic fibrosis

Project description:Purpose: Cystic fibrosis (CF)-associated liver disease (CFLD) is a hepatobiliary complication of CF. Current diagnostic modalities rely on non-specific assessments, while liver biopsy is the gold standard to assess severity of disease. Using miRNA-sequencing we investigated the use of serum miRNA to diagnose and monitor CFLD progression in children with CF. Methods: This was a cross-sectional cohort study of the circulatory miRNA signature of 90 children grouped by clinical, biochemical and imaging assessments as follows: healthy controls (n=30), CF patients with no evidence of liver disease (CFnoLD, n=30) and CFLD (n=30). Serum miRNAs were analysed by miRNA-sequencing. Following total circulatory RNA extraction, RNA samples were pooled together to create three libraries (i.e., 10 patients/library) per study cohort. Libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol (Thermo Fisher, Revision E) and sequenced on the Ion Proton System, using the Ion PI Chip v3 following the Ion PI Hi-Q Sequencing 200 Kit protocol (Thermo Fisher, Revision C). Selected differentially expressed serum miRNA candidates were further validated in 124 individual children serum samples by qRT-PCR and statistical analysis performed to evaluate utility to predict CFLD and hepatic fibrosis severity validated by liver biopsy. Results: The nine libraries sequenced by the Ion Proton System produced 64,658,545 total reads. During processing of the sequencing data, we noticed significant low counts mapped from the CFnoLD library 3. Following principal component analysis this library was confirmed to be an outlier and excluded from the analysis. For the remaining libraries, initial threshold filtering was performed by discarding miRNAs with 10 or less counts and normalized for compositional bias in sequenced libraries and library size. After threshold filtering, 659 miRNAs were identified with a minimum average count of 10.

2018-07-27 | GSE111754 | GEO

Epigenomic profiling of circulating chromatin to detect and monitor squamous transformation in prostate cancer

Project description:Epigenomic profiling of circulating chromatin to detect and monitor squamous transformation in prostate cancer

| PRJNA1232815 | ENA

miRNA expression profiling in Cystic Fibrosis Airway Epithelium

2010-03-23 | GSE19431 | GEO

miRNA expression profiles in Pancreatic Cystic tumours and Pancreatic Cancer

Project description:MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with premalignant lesions. We wished to identify miRNA expression profiles in pancreatic cystic tumors with low malignant potential (serous microcystic adenomas) and high malignant potential (mucinous cystadenoma and intraductal papillary mucinous neoplasm (IPMN)) and compare these to PDAC and carcinoma-ex-IPMN (CEI). n= 20 samples Benign Pancreatic Cystic Tumour (n=7 Microcystic, n= 6 Mucinous, n= 7 IPMN) were compared with n= 9 samples of carcinoma ex IPMN and n= 14 samples of pancreatic cancer (adenocarcinoma) for known homo sapiens miRNAs (mirbase 13).

2011-05-18 | E-GEOD-29352 | biostudies-arrayexpress

miRNA expression profiles in Pancreatic Cystic tumours and Pancreatic Cancer

2011-05-18 | GSE29352 | GEO

miRNA expression profiling in Cystic Fibrosis Airway Epithelium

Project description:Cystic fibrosis (CF) is one of the commonest lethal genetic diseases in which the role of microRNAs (miRNAs) has yet to be explored. We hypothesized that unique miRNA expression profiles exist in CF versus non-CF bronchial epithelial cells so the our aim was to investigate whether unique miRNA expression profiles exist in CF, particularly in CF bronchial epithelial cells and explore their effects on influencing signaling pathways. The expression of 667 miRNAs were measured in bronchial brushings from individuals with and without cystic fibrosis (CFn=5, non-CF n=5). The 5 CF patient samples have been normalised to the controls so we get a final normalised value for 5 samples only. There are 2 raw data files for samples and controls as there are two cards A and B ran for each sample, for a total of 4 raw data files available on the Series record.

2010-03-22 | E-GEOD-19431 | biostudies-arrayexpress

Epigenomic profiling of circulating chromatin to detect and monitor squamous transformation in prostate cancer

Project description:Transformation to squamous cell carcinoma is a rare resistance mechanism in patients with advanced prostate cancer that impacts both prognosis and treatment. Herein, we profile circulating chromatin in serial plasma samples collected from a patient with metastatic prostate cancer that experienced squamous transformation. We detect dynamic changes in gene regulation from circulating chromatin reflecting the emergence of squamous differentiation, enabling non-invasive diagnosis and monitoring of this resistance phenotype.

2025-07-06 | GSE291318 | GEO

Detect-seq on transfected HEK293T cells [Detect-seq data]

Project description:Detect-seq on transfected HEK293T cells [Detect-seq data]

| PRJNA727322 | ENA

Colorectal Cancer Screening in Cystic Fibrosis

Project description:This multi-center study will compare multi-target DNA and quantitative FIT stool-based testing to colonoscopy in individuals with Cystic Fibrosis (CF) undergoing colon cancer screening with colonoscopy. The primary endpoint is detection of any adenomas, including advanced adenomas and colorectal cancer (CRC).

| 2726863 | ecrin-mdr-crc

Proteomics analysis of cystic fluid from human cystic papillary thyroid carcinoma

Project description:Here we have performed quantitative and qualitative profiling of the proteome of cystic fluid from human cystic papillary thyroid carcinoma with the aim to identify specific proteins and pathways involved in cystic fluid from human cystic papillary carcinoma, as well as possible diagnostic markers.

2015-05-20 | PXD000996 | Pride

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