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RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II

ABSTRACT: RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II

PROVIDER: PRJEB46736 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6389070_1.fastq.gz	Fastqsanger.gz
	ERR6389070_2.fastq.gz	Fastqsanger.gz
	ERR6389080_1.fastq.gz	Fastqsanger.gz
	ERR6389080_2.fastq.gz	Fastqsanger.gz
	ERR6389090_1.fastq.gz	Fastqsanger.gz

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RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II

Project description:Ascites or solid tumour from patients with ovarian cancer was collected and grown in culture as ex vivo models. Each sample has a tumour component and some samples have matched stromal cells, which were separated into individual cultures. RNA-seq was performed on these models to establish gene expression profiles, which allow the assessment of the separation protocol and identification of genes that are differentially expressed. The histological subtype from which the models were collected includes majorly high-grade serous, but also low-grade serous, clear cell and mucinous ovarian cancer. The sample subtypes have been assessed using a machine-learning based transcriptional classifier. These samples are processed in the same manner as a previous study, “E-MTAB-7223 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells”

2021-08-05 | E-MTAB-10801 | biostudies-arrayexpress

RNA-seq of human ex vivo ovarian cancer models - part III

Project description:Ascites or solid tumour samples from patients with ovarian cancer were collected and grown in culture as ex vivo models of purified tumour cells. RNA-seq was performed on these models to establish gene expression profiles, which allow identification of genes that are differentially expressed between patients with differing tumour intrinsic properties. These samples have been interrogated for the presence of a gene expression signature indicative of sensitivity to an inhibitor of poly(ADP-ribose) glycohydrolase (PARG). These samples are processed in the same manner as previous studies: “E-MTAB-7223 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells” and “E-MTAB-10801 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II” with no stromal counterparts included in this current sequencing batch.

2021-10-10 | E-MTAB-11000 | biostudies-arrayexpress

Exome sequencing of human ex vivo ovarian cancer models with matched stromal cells

Project description:Ascites or solid tumour from patients with ovarian cancer was collected and grown in culture as ex vivo models. Each sample has a mixture of tumour and stromal cells which were separated into individual cultures. Therefore each patient has tumour and stromal cultures originating from the same tissue collection. Variant calling (exome-seq) analysis was performed on these matched models to establish tumour specific mutations. Stromal cells were used to rule out germline mutations.

2020-03-13 | E-MTAB-7225 | biostudies-arrayexpress

RNA-seq of human ex vivo ovarian cancer models with matched stromal cells

Project description:Ascites or solid tumour from patients with ovarian cancer was collected and grown in culture as ex vivo models. Each sample has a mixture of tumour and stromal cells which were separated into individual cultures. Therefore each patient has tumour and stromal cultures originating from the same tissue collection. RNA-seq was performed on these matched models to establish gene expression profiles which allow the assessment of the separation protocol and establish genes that are differentially expressed for use in future validation processes.

2020-03-13 | E-MTAB-7223 | biostudies-arrayexpress

RNA-seq of human ex vivo ovarian cancer models with matched stromal cells

Project description:RNA-seq of human ex vivo ovarian cancer models with matched stromal cells

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Exome sequencing of human ex vivo ovarian cancer models with matched stromal cells

Project description:Exome sequencing of human ex vivo ovarian cancer models with matched stromal cells

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Single cell RNA-seq of a human ex vivo ovarian model with matched stromal cells

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RNA-seq of human ex vivo ovarian cancer models - part III

Project description:RNA-seq of human ex vivo ovarian cancer models - part III

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Single cell RNA-seq of a human ex vivo ovarian model with matched stromal cells

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Transcriptomic analysis of patient-derived ex vivo models of pancreatic cancer

Project description:The aim of this study is to compare the transcriptomic profiles of various ex vivo models of pancreatic cancer. First, primary tumours and their corresponding xenografts in nude mice were analysed by RNA-seq. Monocultures of pancreatic cancer cells derived from the xenografts were then prepared as 2D monolayers, Matrigel-embedded organoids, spheres in suspension and 3D cultures in self-assembling peptide amphiphile (PA) hydrogels. Seven-day cultures were then analysed by RNA-seq. The results suggest that all ex vivo monocultures retain patient-specific transcriptional profiles, especially cancer stem cell signatures, while being deficient in the expression of stromal components such as the core matrisome. Correlations with the primary tumours were generally higher in PA hydrogels than organoids. Biased gene expression signatures were identified in certain models. This is the first study to explore the transcriptomic signatures of four different ex vivo models matched to their primary tumours of origin.

2021-07-03 | GSE139184 | GEO

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