Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylome and gene expression profiling of paired primary cancer and liver metastasis from colorectal cancer patients

ABSTRACT: We generated reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-Seq) data of 20 samples (paired primary and liver metastases from 10 CRC patients) to understand key molecular events involved in tumor progression and metastasis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213402 | GEO | 2023/08/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of paired primary and metastatic cell lines identifies common DNA methylation changes in melanoma metastasis.

Project description:Using 1 melanocyte and 6 melanoma cell line (3 pair of primary and metastatic), we generated base-resolution DNA methylation maps to document DNA methylation drivers of melanoma metastasis. Here we generated single-nucleotide resoultion DNA methylation map of a total of 7 cell lines using Reduced Representation Bisulfite Sequencing (RRBS)

2017-05-17 | E-GEOD-70621 | biostudies-arrayexpress

The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

Project description:We conducted reduced representation bisulfite sequencing (RRBS) on myonuclei and interstitial nuclei and observed stark differences in methylation patterns during adaptation

2020-04-13 | GSE144774 | GEO

Expression data from miRNAs in colorectal cancer tissues with and without liver metastasis

Project description:The purpose of this study is to identify miRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 39 miRNAs were identified to be differentially expressed between 16 primary CRC tissues with liver metastases and 16 CRC tissues without liver metastases from 32 patients by Affymetric miRNA microarrays. 16 coloretcal cancer tissues with liver metastasis and 16 colorectal cancer tissues without liver metastasis were included in this study for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the differentially expressed miRNAs between colorectal cancer tissues with and without liver metastasis.

2013-12-10 | E-GEOD-53159 | biostudies-arrayexpress

Modeling Tumor Development and Metastasis using Paired Organoids Derived from Patients with Colorectal Cancer Liver Metastases

Project description:Tumor metastasis accounts for the majority of cancer-related deaths; it is therefore important to develop preclinical models that faithfully recapitulate disease progression. Here, we generated paired organoids derived from primary tumors and matched liver metastases in the same colorectal cancer patients (CRC). Despite the fact that paired organoids exhibit comparable gene expression and cell morphology. organoids from metastatic lesions demonstrate more aggressive phenotypes, tumorigenesis, and metastatic capacity than those from primary lesions. Transcriptional analyses of the paired organoids reveal signature genes and pathways altered during the progression of CRC. including SOX2, altered during the progression of CRC. Further study shows that inducible knockdown of SOX2 attenuated invasion, proliferation, and liver metastasis outgrowth. Taken together, we use patient-derived organoids to model cancer metastasis. Our data propose that SOX2 is not only a critical biomarker for the development and metastasis of CRC, but also a potent target for the disease treatment.

2020-10-05 | GSE148918 | GEO

Expression data from miRNAs in colorectal cancer tissues with and without liver metastasis

2013-12-10 | GSE53159 | GEO

Downregulation of microRNA-132 is associated with liver metastasis of colorectal cancer by targeting Anoctamin 1.

Project description:In this study, we conducted a microarray-based analysis to identify differentially expressed miRNAs in CRC by comparing miRNA profiles among primary CRC tissues from patients with liver metastases, primary tissues without liver metastases, and liver metastatic lesions. microRNAs (miRNAs) have been shown to have a potential for cancer diagnosis lately. The main objective of this study is to identify a novel biomarker serum miRNA from the patients with colorectal cancer (CRC). Microarray analysis of miRNA expression was performed using paired pre- and post- operative serum from 10 CRC patients. Two miRNAs (let-7a, miR-199a-3p) decreased significantly in the post-operative serum when compared to pre-operative serum (P=0.015 and 0.029, respectively). Microarrays were performed for the testing cohort of primary CRC lesions (n=28) and liver metastatic lesions (n=8).

2016-02-14 | E-GEOD-72199 | biostudies-arrayexpress

Murine mammary epithelial cell methylome and ATAC-seq analyses

Project description:The following data comes from two separate experiments. In the initial experiment, luminal and basal murine mammary epithelial cells were analyzed by reduced representation bisulfite sequencing (RRBS) to generate methylome profiles. In the second experiment, luminal and basal murine mammary epithelial cells were analyzed by ATAC-seq.

2018-06-10 | GSE80181 | GEO

Single-cell chromatin accessible state of paired primary and liver metastasis colorectal cancer cells from PDX cells derived mouse model

Project description:Chromatin regulatory networks that maintain differentiated cell states are frequently dysregulated in and thus contribute to cancer metastasis. Here, we reveal the dynamic transitions of regulatory states of colorectal cancer (CRC) cells during metastasizing to liver by profiling single-cell chromatin accessibility of paired primary and metastatic CRC tumors in mouse. We discover CRC subclones, which are characterized by losing chromatin accessibility around colon-tissue specific genes and gain that around liver-specific genes,including transcription factors in FOXA family and HNF family we discovered in our previous study, might partially mimic types of liver cells across the liver development. A particular subclone with stem-like state, which is highly enriched in metastases but not primary tumors , clearly shows poor prognosis.

2023-04-01 | GSE200813 | GEO

Assessing the influence of DNMTi on human CD8+ T cells on a global level using methylome and transcriptome analyses.

Project description:RRBS (Reduced Representation Bisulfite Sequencing) and RNA-seq were performed on human CD8+ T cells from peripheral blood of three independent healthy donors to study the influence of DNMTi on CD8+ T cells on a global level.

2021-02-08 | GSE93383 | GEO

DNA methylation analysis of colorectal cancer SW48/YB5 cell line treated with the HH1 compound

Project description:YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving expression of a GFP reporter. The cells were treated with 10 micromolar concentration of the HH1 compound or with DMSO as a control. Reduced representation bisulfite sequencing (RRBS) was performed after the treatment to analyze DNA methylation at CpG sites.

2018-07-31 | GSE104998 | 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