GEO DataSets

(Submitter supplied) In Rspondin-based three-dimensional cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. Here we report the establishment of tumor organoid cultures from 20 consecutive colorectal carcinoma (CRC) patients. For most, organoids were also generated from adjacent normal tissue. Organoids closely resemble the original tumor. The spectrum of genetic changes within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

108 Samples

Download data: CSV

(Submitter supplied) In Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. We report the establishment of tumor organoid cultures from 20 consecutive colorectal (CRC) patients. For most, organoids were also generated from adjacent normal tissue. The organoids closely resemble the original tumor. The spectrum of genetic changes observed within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

37 Samples

Download data: CEL

(Submitter supplied) Kidney tumours are among the most common solid tumours in children, comprising several distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first paediatric cancer organoid biobank. It contains tumour and matching normal kidney organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumours, malignant rhabdoid tumours, renal cell carcinomas, and congenital mesoblastic nephromas. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

45 Samples

Download data: IDAT, 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) The study of human liver cancer has been hampered by the lack of reliable models that faithfully recapitulate the physiopathology of the patient’s original tumour ex vivo. Here, we describe the first culture system to allow the establishment and long-term expansion of human primary liver cancer (PLC) organoids (called tumoroids) from the three most common PLC subtypes: Hepatocellular carcinoma (HCC), Cholangiocarcinoma (CC) and mixed HCC/CC tumours (CHC). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18460 GPL20301

59 Samples

Download data: TXT, VCF

(Submitter supplied) Purpose: Colorectal cancer (CRC) patients with peritoneal metastases (CRPM) have limited treatment options and the lowest CRC survival rates. We aimed to determine whether organoid testing could help guide precision treatment for CRPM patients, as the clinical utility of prospective, functional drug screening including non-standard agents is unknown. Experimental Design: CRPM organoids (peritonoids) isolated from patients underwent parallel next-generation sequencing and medium-throughput drug panel testing ex vivo to identify specific drug sensitivities for each patient. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

17 Samples

Download data: CSV

(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) 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) We present TORNADO-seq —a high-throughput, a high-content drug discovery platform that for the first time uses next-generation sequencing (NGS) based, targeted RNA-seq in organoids monitoring the expression of 206 genes for the evaluation of complex mixtures of cellular phenotypes. TORNADO-seq is a fast, highly-reproducible, time- and cost-effective (5$ per sample including sequencing cost) method that we used to find drugs that enrich for differentiated cell phenotypes in intestinal organoids. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1249 Samples

Download data: TXT

(Submitter supplied) Regeneration capacity of intestinal epithelial cells are highly dependent on the status of stemness. In the homeostasis, only a small subset of stem cells is responsible for the turnover of the intestinal epithelium. However, at the injury, such as caused by radiation, intestinal epithelial cells show substantial plasticity for regeneration. Most of the colorectal cancers (CRCs) are differentiated adenocarcinoma, which maintain the expression of both stemness and differentiation markers, suggesting an existence of a similar regeneration system as in normal cells, although the role of such fluctuation of stemness in regeneration of cancer after irradiation is not well understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

8 Samples

Download data: TXT

(Submitter supplied) Organoid technology provides the possibility to culture human colon tissue and patient-derived colorectal cancers (CRC) while maintaining all functional and phenotypic characteristics. Labeling of human colon stem cells (CoSCs), especially in normal and benign tumor organoids, is challenging and therefore limits usability of multi-patient organoid libraries for CoSC research. Here, we developed STAR (STem cell Ascl2 Reporter), a minimal enhancer/promoter element that reports transcriptional activity of ASCL2, a master regulator of LGR5+ CoSC fate. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

(Submitter supplied) Here we compare RNA expression profiles of colorectal cancer organoids grown in four different conditions, namely standard organoids medium, minimal medium without growth factors or with normal or cancer associated fibroblasts. We found majorly different expression profiles between conditions and more heterogeneous tumor cell population in organoids grown with fibroblasts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

72 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

58 Samples

Download data: TXT

(Submitter supplied) Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serves as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer.To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serve as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer. To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

52 Samples

Download data: TXT

(Submitter supplied) Although the anti-cancer properties of Oligomeric Proanthocyanidins (OPCs) from grape seeds has been well recognized, the molecular mechanisms by which they exert anti-cancer effects are poorly understood. In this study, through comprehensive RNA-sequencing based gene-expression profiling in multiple colorectal cancer cell lines, we for the first time illuminate the genome-wide effects of OPCs from grape seeds in colorectal cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

Download data: CSV

(Submitter supplied) The broad research use of organoids from high-grade serous ovarian carcinoma (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here we describe a method for generation and long-term expansion of HGSC organoids with efficacy markedly improved over previous reports (53% vs. 23-38%). We established organoids from cryopreserved material, demonstrating the feasibility of using viably biobanked tissue for HGSC organoid derivation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301 GPL24676

22 Samples

Download data: TSV

(Submitter supplied) We analyzed gene expression of 58 line patinet-derived colorectal tumors and normal organoids.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16043

58 Samples

Download data: CEL

(Submitter supplied) Gene expression profiles after treatment with the DNA methylation inhibitor 5-Aza-CdR and DNMT1 knockdown were analyzed in tumor organoids derived from ApcMin mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL5642

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

134 Samples

Download data