Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

78 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Ian Donaldson

PROVIDER: E-MTAB-7223 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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 - 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

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

Single cell RNA-seq from 10X for a living biobank of ovarian cancer ex vivo models reveals profound mitotic heterogeneity

Project description:We validated fifteen models from “living biobank” to provide models that support interrogation of Chromosome Instability and to evaluate novel therapeutics. Single cell RNA-seq was performed on tumour and stromal cells from 4 patients with ovarian cancer to establish gene expression profile differences between the two cell types and also heterogeneity within the tumour population. The samples used were AS38b, AS59, AS74-1, AS79, they are grown in OCMI media supplemented with 5% hyclone serum (AS38, AS59) or 5% FBS (AS74, AS79) in 5% CO2 and 5% O2. At 37C

2020-01-23 | E-MTAB-8559 | biostudies-arrayexpress

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

Project description:single cell RNA-seq was performed on tumour and stromal cells from a single patient with ovarian cancer to establish gene expression profile differences between the two cell types and also heterogeneity within the tumour population.

2020-01-16 | E-MTAB-7249 | biostudies-arrayexpress

Lineage plasticity in SCLC generates non-neuroendocrine cells primed for vasculogenic mimicry

Project description:RNA-seq data characterising neuroendocrine (NE) and non-NE cells, cultured on plastic or Matrigel, extracted from small cell lung cancer circulating tumour cell derived explants.

2023-09-17 | E-MTAB-10950 | biostudies-arrayexpress

RNA-Seq of murine head and neck cancer cell line (MOC1) treated with antiPD-L1 antibody with or without an adenovirus encoding TNFa and IL-2

Project description:We investigated changes to the head and neck tumour microenvironment immune cell transcriptome following treatment with an adenovirus encoding TNFa and IL-2 in the context of a antiPD-L1 refractory model. Murine head and neck cancer cell line was engrafted subcutaneously onto the right flank of immunocompetent mice. Tumours were treated with antiPD-L1 until 'refractory' status as determined by tumour volume. The tumours were than treated with or without an adenovirus encoding TNFa and IL2. Tumours were digested and CD45+/- were isolated using magnetic bead isolation.

2022-03-09 | E-MTAB-11204 | biostudies-arrayexpress

Methylation profiling of chondrosarcoma tumour samples

Project description:Methylation profiling of IDH WT, IDH1 and IDH2 mutated chondrosarcoma tumour samples

2022-03-01 | E-MTAB-11031 | biostudies-arrayexpress

Methylation profiling (450K and EPIC array) for sarcoma classification

Project description:Infinium® HumanMethylation450 BeadChip and EPIC arrays were run with the aim of using the methylation profiles (n=986 in total) for sarcoma subtype classification (Paper: Lyskjær et al, 2021, DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the ‘DKFZ sarcoma Classifier’ ). 500ng of DNA from fresh frozen (FT) or formalin-fixed paraffin-embedded (FFPE) tumour samples were bisulfite converted using the Zymo EZ DNA methylation Gold kit (Zymo Research Corp. Irvine, USA) before hybridisation to the Infinium HumanMethylation450 or EPIC beadchip arrays (Illumina, San Diego, CA) by UCL Genomics. All bisulfite-converted FFPE samples were restored with the Infinium FFPE DNA Restore kit (Illumina).

2021-05-01 | E-MTAB-9875 | biostudies-arrayexpress

Prognostic whole-genome and transcriptome signatures in colorectal cancers

Project description:Colorectal cancer is the third most common and the second deadliest tumour type in both sexes world-wide. To understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. High quality transcriptome sequences from 1,063 tumours and 120 tissue normals enabled integration analyses of gene mutations and gene expression levels.

2024-05-15 | E-MTAB-12862 | biostudies-arrayexpress

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