Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile of colorectal cancer tissues from 87 patients

ABSTRACT: Colorectal cancer organoids (CCOs) recapitulate the gene expression signatures of their respective primary tumors. These CCOs provide valuable model for studying the primary cancers.

ORGANISM(S): Homo sapiens

PROVIDER: GSE171680 | GEO | 2021/07/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression profiles of colorectal cancer organoids from 87 patients

Project description:Colorectal cancer organoids (CCOs) recapitulate the gene expression signatures of their respective primary tumors. These CCOs provide valuable model for studying the primary cancers.

2021-07-20 | GSE171681 | GEO

Pancreas Cancer Organoid Profiling

Project description:<p>We generated a collection of patient-derived pancreatic normal and cancer organoids. We performed whole genome sequencing, targeted exome sequencing, and RNA sequencing on organoids as well as matched tumor and normal tissue if available. This dataset is a valuable resource for pancreas cancer researchers, and those looking to compare primary tissue to organoid culture. In our linked publication, we show that pancreatic cancer organoids recapitulate the mutational spectrum of pancreatic cancer. Furthermore, RNA sequencing of organoids demonstrates the presence of both transcriptional subtypes of pancreas cancer.</p>

| phs001611 | dbGaP

mRNA expression data from adenoma, gene modified, and colorectal cancer organoid.

Project description:We established human colorectal tumor organoids from benign adenoma, primary colorectal cancer or metastasized colorectal cancer. The gene signature of tumor organoids associated with their tumor progression status. We also generated genome-edited organoids from human intestinal organoids recapitulating adenoma-carcinoma sequence. Gene expression signature of the genome engineered organoids were similar to that of adenoma organoids. This result indicated multiple (up to five) genetic mutations were insufficient for gene expression reprogramming of colorectal cancer. We used microarrays to detail the global program of gene expression in human colorectal tumor organoids and artificially mutation introduced organoids. To assess the expression profiling of genome-engineered organoids, we prepared total-RNA from cultured adenoma, carcinoma and genome-engineered organoids. We produced two types of genome-engineered organoids using the CRISPR/Cas9 or lentivirus vector system. Each engineered gene and engineered methods are described as a single alphabet and method name, respectively, in the sample characteristics field. The abbreviations for the engineered genes are as follows. 1) Genome-engineered organoids with CRISPR/Cas9 A = APC deletion; K = KRAS G12V knock in; S = Smad4 deletion; T = TP53 deletion; P = PIK3CA E545K knock in. 2) Genome-engineered organoids with Lent virus vector B = CTNNB1 S33Y overexpression; K = KRAS G12V overexpression; S = Smad4 shRNA overexpression; T = TP53 shRNA overexpression; P = PIK3CA E545K overexpression.

2015-01-18 | E-GEOD-57965 | biostudies-arrayexpress

mRNA expression data from adenoma, gene modified, and colorectal cancer organoid.

2015-01-18 | GSE57965 | GEO

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

Identification of gene signature in human colorectal CD44+ cancer stem cells

Project description:We prospectively isolated human colorectal CD44+ cancer stem cells (CSCs) from organoids and primary colorectal cancer. The gene expression of CD44+ CSCs are relevant to each other between organoids and primary tissues. The common gene signature in two different modality identifies CSCs' properties with the biological significance shown in original article.

2018-11-09 | GSE100433 | GEO

Gene expression profiles of colorectal cancer organoids from 87 patients

Project description:Gene expression profiles of colorectal cancer organoids from 87 patients

| PRJNA720565 | ENA

Single cell 3' RNA sequencing of 23 Korean colorectal cancer patients

Project description:For the understanding intrinsic cancer cell signatures and the surrounding microenviroment, we provide single-cell 3' RNA sequencing dataon 63,689 cells from 23 CRC patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analysis of primary colorectal cancer and normal mucosa samples depicts a comprehensive cellular landscape of colorectal cancer and potential cellular interaction, which would be a valuable resource for the development of therapeutic strategies.

2020-04-04 | GSE132465 | GEO

FBXW4 acts as a protector of FOLFOX-based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-expression network analysis

Project description:To measure global gene expression in primary metastatic colorectal cancer patients who have undergone fluorouracil, leucovorin and oxaliplatin (FOLFOX) chemotherapy and screen valuable biomarkers to predict the effects of chemotherapy. Samples from primary metastatic colorectal cancer patients were collected. The effects of chemotherapy were evaluated.

2020-01-28 | GSE138912 | GEO

Integrated -Omics Analyses Demonstrate that Patient-Derived Colon Organoids Faithfully Recapitulate the Tumor Tissue of Origin, Highlighting Altered Pathways in Colorectal Cancer Progression

Project description:Purpose: methodically characterize colorectal cancer patient-derived organoids, at the molecular level, under different culturing conditions, by evaluating genomic, transcriptomic and phosphoproteomic profiles in order to define their ability to stably recapitulate patients-derived tissues features. Outcome: integrated molecular and bioinformatics analyses demonstrated that PDCOs faithfully recapitulate the tumor tissue of origin. Our results indicate that the in vitro culture of biopsy-derived organoids does not introduce substantial variation in the genomic landscape of CRC but still promotes the expansion of the more aggressive subset of cancer cells. In conclusion, our findings strongly support the use of CRC organoids as a novel and very promising and stable tool for personalized medicine that could represent a powerful alternative to animal experimentation in vivo.

2021-06-22 | GSE157004 | 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