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Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

ABSTRACT: Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

PROVIDER: PRJNA255123 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1513860_1.fastq.gz	Fastqsanger.gz
	SRR1513860_2.fastq.gz	Fastqsanger.gz
	SRR1513861_1.fastq.gz	Fastqsanger.gz
	SRR1513861_2.fastq.gz	Fastqsanger.gz
	SRR1513853_1.fastq.gz	Fastqsanger.gz

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Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [meDIP-seq]

Project description:Validation of methylation data for 9 osteosarcoma Patient tumours and PDXs by MeDIP followed by next generation sequencing 9 samples, MeDIP done with Diagenode kit and libraries prepped using NEB kit, sequenced on HiSeq 2000

2014-11-26 | E-GEOD-59351 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [meDIP-seq]

Project description:Validation of methylation data for 9 osteosarcoma Patient tumours and PDXs by MeDIP followed by next generation sequencing

2014-11-26 | GSE59351 | GEO

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [methylation profiling by array]

Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in Osteosarcoma and Colon Cancer PDXs Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

2014-11-26 | E-GEOD-59134 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [methylation profiling by array]

Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in Osteosarcoma and Colon Cancer PDXs

2014-11-26 | GSE59134 | GEO

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics.

Project description:BackgroundThe use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics.MethodsIn this study, we assessed the suitability of patient-derived tumour xenografts (PDXs) for methylome analysis using Infinium 450 K Beadchips and MeDIP-seq.ResultsControlled for confounding host (mouse) sequences, comparison of primary PDXs and matching patient tumours in a rare (osteosarcoma) and common (colon) cancer revealed that an average 2.7% of the assayed CpG sites undergo major (Δβ ≥ 0.51) methylation changes in a cancer-specific manner as a result of the xenografting procedure. No significant subsequent methylation changes were observed after a second round of xenografting between primary and secondary PDXs. Based on computational simulation using publically available methylation data, we additionally show that future studies comparing two groups of PDXs should use 15 or more samples in each group to minimise the impact of xenografting-associated changes in methylation on comparison results.ConclusionsOur results from rare and common cancers indicate that PDXs are a suitable discovery tool for cancer epigenomics and we provide guidance on how to overcome the observed limitations.

| S-EPMC4292812 | biostudies-literature

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-26 | E-GEOD-59352 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

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

2014-11-26 | GSE59352 | GEO

Basal transcriptome profiles of breast cancer PDXs.

Project description:Basal transcriptome profiling of breast cancer patient-derived xenografts (PDXs) as a resource to identify predictive biomarkers of target therapeutic approaches.

2020-05-13 | GSE148310 | GEO

mRNA sequencing of highly and lowly metastatic human colorectal cancer PDXs

Project description:We performed in-vivo selection of human patient derived colorectal cancer xenografts. 4 independent highly-liver metastatic sub-lines (lvm PDXs) were generated. Those lvm PDXs were harvested with the corresponding parental PDX tumors from mice and then we performed MACS mice cell depletion followed by FACS sorting to obtain human EpCAM positive and mice MHC negatitve populations. total RNA was extracted from those ex-vivo tumors and high-throuput sequencing was performed

2019-10-02 | GSE138248 | GEO

RNA-Seq of MSK-PCa series of Patient Derived Organoids and Xenografts

Project description:Transcriptome profiling analysis was performed in 22 human prostate cancer organoids, 6 patient-derived xenografts (PDXs) and 7 cell lines.

2021-08-04 | GSE181374 | GEO

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