GEO DataSets

(Submitter supplied) To develop a better understanding of the biology underlying risk for CRC posed by germ line APC mutations we performed DNA methylation analysis of colon organoids derived from normal-appearing colons of FAP subjects (n=7) and matched healthy individuals (n=16). We identified a large number (n=358) of differentially methylated regions (DMRs) between colon organoids of FAP and healthy subjects, many of which were also identified in a comparison of tumor and normal adjacent tissue (NAT) in two independent, sporadic CRC tumor cohorts.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

23 Samples

Download data: CSV, IDAT

(Submitter supplied) Here, we generated bulk RNA-seq data on colon organoids derived from both healthy and familial adenomatous polyposis patients. We related findings observed within this dataset to differential expression findings from a publicly available colorectal cancer cohort.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

13 Samples

Download data: CSV

(Submitter supplied) mRNA expression from tubular adenomas of patients with Familial Adenomatous Polyposis

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: TXT

(Submitter supplied) Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) In this study, we performed whole transcriptomics analysis (RNA-seq) in a cohort of colorectal polyps and the matched normal tissue in FAP patients, which reveals a significant activation of inflammatory and cell proliferation pathways.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Wnt signaling plays a pivotal role in colorectal cancer. Intrinsic activation of Wnt by mutational events, such as mutations in the tumor suppressor gene APC, represents the most frequent initiating event in this disease background. Long truncated versions of APC retain partial functionality, which leads to a sub-maximal, “just right” activation state of Wnt signaling supposed to be beneficial for disease initiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Gastric adenocarcinoma and proximal polyposis of the stomach is an autosomal dominant cancer predisposition syndrome of fundic gland polyposis with a significant risk of gastric adenocarcinoma. We mapped the gene to 5q22 and found loss of heterozygosity (LOH) only on 5q in fundic gland polyps from affected individuals. Sanger sequencing revealed novel point mutations in APC promoter 1B that co-segregated with disease. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18952

14 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation of 23 familial adenomatous polyposis tumors. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) To identify the gene expression of early-onset colorectal cancer, we sampled early-onset colorectal cancer patients (age < 50) and late-onset colorectal cancer paitients (age > 70) We then performed gene expression profiling analysis using data obtained from RNA-seq of early-onset colorectal cancer tissues and late-onset colorectal cancer tissues.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

99 Samples

Download data: TXT

(Submitter supplied) Extracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

8 Samples

Download data: TXT

(Submitter supplied) Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: CSV

(Submitter supplied) Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Here, we used bulk RNA-seq data derived from healthy colon organoids exposed to two differing calcium concentrations. Through the use of external single cell RNA-seq data, we estimate changes in cell composition and gene expression brought about by high calcium conditions and relate those effects to colorectal cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

72 Samples

Download data: CSV

(Submitter supplied) RNA sequencing of duodenal polyps in FAP patients treated with plabebo or the drug combination, erlotinib + sulindac

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

69 Samples

Download data: XLSX

(Submitter supplied) Numerous demographic factors have been associated with colorectal cancer (CRC) risk, with age, body mass index, smoking history, sex, and differences in ancestry, among the most consistent. However, biological mechanisms underlying these associations remain unclear. Limitations of traditional cancer models, such as animal models and CRC cell lines, and the large data dispari-ty between European American and minority groups present challenges in relating mechanisms to the average-risk population. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

15 Samples

Download data: CSV

(Submitter supplied) Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the im-portant role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA), and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epige-nome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n=140 samples)

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

140 Samples

Download data: IDAT, TXT

(Submitter supplied) We analyzed gene expression of 3 lines of patient-derived colorectal cancer organoids.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

3 Samples

Download data: CEL

(Submitter supplied) Background & Aims: Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer; yet, mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility. Methods: Human colonic organoids from one individual were cultured and treated in triplicate with 3mM ASA or vehicle control (DMSO) for 24 hours. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

12 Samples

Download data: NARROWPEAK, RESULTS

(Submitter supplied) To identify genes and molecular pathways involved in colorectal cancer (CRC) that developed in an inflammatory microenvironment, we performed Sleeping Beauty (SB) transposon mutagenesis screening in Dextran Sodium Sulfate treated-mice. We have shown that cell cycle-related genes and TGFb pathway-related genes are frequently mutated in inflammation-related tumors. We have demonstrated that TNFa can promote dedifferentiation of colonic epithelial cells via epigenomic reprogramming, and activate both Cdkn2a-p53 signaling and CycD-Cdk4/6, creating advantageous conditions for selecting cells carrying mutations in the Cdkn2a-p53 pathway genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

26 Samples

Download data