Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [DNA-seq]

ABSTRACT: We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

ORGANISM(S): Homo sapiens

PROVIDER: GSE186573 | GEO | 2023/09/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [miRNA-seq]

Project description:We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

2023-09-28 | GSE186595 | GEO

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA]

2023-09-28 | GSE186587 | GEO

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [MeDIP-seq]

2023-09-28 | GSE186575 | GEO

Cell-Free RNA Signature for Noninvasive Diagnosis of Hepatocellular Carcinoma Using MOF to Enrich Circulating Nucleic Acids

Project description:We developed a new method to extract cfNA (containing cfDNA, cfRNA and viral RNA) from serum/plasma based on the adsorption of nucleic acids by MOF materials (Co-IRMOF-74-IV), and compared the extraction capability with commercial kit method. We conducted a comprehensive characterization of the cell-free RNA in a small number of clinical samples, including patients with HCC (n=14), CHB (n=17) and normal individuals (n=8). And then we build a model with 6 cfRNA signature to diagnose liver cancer, and indicated high diagnostic efficiency (AUC=0.905) in the independent validation cohort (HCC n=7, CHB n=4 and normal individuals n=8)

2023-08-01 | GSE210775 | GEO

Cancer specific microbiome revealed by cell-free RNA reads in patients' plasma

Project description:We sequenced cell-free RNA (cfRNA) for five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer and esophageal cancer) and healthy individuals in 230 plasma samples collected from 6 clinical centers in China. Cancer related signaling pathway and microbial genus were identified. Cancer detection and specific classification were achieved through combining both host and microbial cfRNA reads.

2022-07-12 | GSE174302 | GEO

Liquid Biopsy Evaluation and Repository Development at Princess Margaret

Project description:The objective of this protocol is to develop an institution-wide liquid biopsy protocol that will establish a common process for collecting blood and corresponding archived tumor specimens for future research studies at the University Health Network’s Princess Margaret Cancer Centre. Circulating cell-free nucleic acids (cfNA), including cell-free DNA (cfDNA) and cell-free RNA (cfRNA), are non-invasive, real-time biomarkers that can provide diagnostic and prognostic information before cancer diagnosis, during cancer treatment, and at disease progression. Cancer research scientists and clinicians at the Princess Margaret are interested in incorporating the collection of peripheral blood samples ("liquid biopsies") into research protocols as a means of non-invasively assessing tumor progression and response to treatment at multiple time points during a patient’s course of disease.

| 2286534 | ecrin-mdr-crc

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA PBMC]

Project description:We sequenced 8 colorectal cancer patients' PBMC samples, and 6 healthy donors' PBMC samples. These individuals' plasma RNA have been profiled.

2023-09-28 | GSE218999 | GEO

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [Tissue RNA-seq]

Project description:We sequenced 30 tissue samples from 15 colorectal cancer patients, including tumor and tumor-adjacent normal tissue (> 2cm from the primary tumor). These patients' plasma has been profiled.

2023-09-28 | GSE211831 | GEO

Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children

Project description:Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C — two conditions presenting with overlapping symptoms — with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.

2024-09-11 | GSE255555 | GEO

Transcriptomic analyses of gastrointestinal function in the “dwarf” and “medium” forms of Sthenoteuthis oualaniensis during sexual maturation

Project description:Sthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the “dwarf” form (DF) and “medium” form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the DF and MF of SA using the deep-sequencing platform Illumina HiSeq™. We exploited a high-throughput method to delineate differentially expressed genes (DEGs) in the DF and MF of SA. A total of 135,464 unigenes (68627 unigenes of the DG and 66837 unigenes of the MF) were generated. We identified 7965 and 4051 relative DEGs in the intestine and stomach tissue of the mature DF of SA compared with those of the immature DF of SA; and 22138 and 18460 DEGs in the intestine and stomach of the mature MF of SA compared with those of the immature MF of SA. Functional categorization and pathway analyses of these DEGs with regard to the metabolism of differentially expressed genes were noted. This work is the first to identify a set of genes associated with gastrointestinal function during the sexual maturation of SA.

2018-05-16 | GSE114458 | GEO

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