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Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [RNA-seq]

ABSTRACT: RNA sequencing demonstrates molecular profiles common to primary tumor, PDX and organoid models

ORGANISM(S): Homo sapiens

PROVIDER: GSE114453 | GEO | 2020/06/01

REPOSITORIES: GEO

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Human Organoids Share Structural and Genetic Features with Primary Pancreatic Adenocarcinoma Tumors.

Project description: Not available

| S-EPMC6647028 | biostudies-literature

Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-06-01 | GSE114455 | GEO

Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [Drop-seq]

Project description:In this study, we applied Drop-seq, a high throughput single cell RNA-seq platform, to characterize the different cell types present in pancreatic cancer organoids. We sequenced the transcriptomes of 7675 single cells from organoids derived from a patient undergoing a Whipple procedure for pancreatic ductal adenocarcinoma (PDAC). We then developed a novel clustering approach based on a class of probabilistic generative models called topic models, leading to the identification of subpopulations of cells.

2020-06-01 | GSE114454 | GEO

Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor

Project description:Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor

| PRJNA471419 | ENA

Establishment and disease modeling of non-small cell lung cancer organoids

Project description:Purpose: The goal of this study is to establish and molecularly characterize non-small cell lung cancer (NSCLC) organoids. Generation of NSCLC organoids would provide additional preclinical models for drug screening and biomarker discovery. Methods: Patient lung tumors and previously established patient-derived xenografts (PDX) were processed to generate organoids. Total RNA was extracted and subjected to RNA-seq to examine the gene expression similarity between patient/PDX/organoid of the same model using t-SNE clustering. Results: Through RNA-sequencing, we generated TPM values of patient, PDX and organoid samples of 5 models. t-SNE analysis showed that the patient/PDX/organoid of the same models clustered together. The lung adenocarcinoma samples formed a separate cluster from the squamous cell carcinoma samples based on gene expression. Conclusions: Our study introduces the establishment of NSCLC organoids and demonstrates the gene expession similarity of the organoid model to its corresponding PDX and patient sample.

2019-11-26 | GSE119004 | GEO

Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

Project description:Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

| PRJNA498740 | ENA

Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

Project description:Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

| PRJNA498741 | ENA

Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [Drop-seq]

Project description:Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [Drop-seq]

| PRJNA471422 | ENA

Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [RNA-seq]

Project description:Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [RNA-seq]

| PRJNA471423 | ENA

Expression Analysis of Mouse Tumor and Metastatic Pancreatic Ductal Adenocarcinoma Organoids

Project description:This study used Illumina strand-specific, paired-end RNA-sequencing to examine gene expression differences between matched murine tumor- and metastasis-derived mouse pancreatic ductal adenocarcinoma (PDAC) cells grown as three-dimensional, organoid cultures. The study analyzed 16 organoid lines derived from matched primary PDAC tumors and PDAC metastases from 6 KPC (KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre) mice.

2020-06-16 | GSE142467 | GEO

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