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Methylation profiling of choroid plexus carcinoma cell lines

ABSTRACT: Methylation profiling of choroid plexus carcinoma cell lines

PROVIDER: PRJNA991505 | ENA |

REPOSITORIES: ENA

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Gene expression data from normal mouse choroid plexus, choroid plexus papilloma and choroid plexus carcinoma

Project description:Atoh1-Cre; Myc/Myc mice developed choroid plexus papilloma and Atoh1-Cre; Myc/Myc; p53fl/fl mice developed choroid plexus carcinoma. By studying the gene expression profiles of normal choroid plexus, choroid plexus papilloma and choroid plexus carcinoma in mice, we aim to gain a better understanding of the biology of choroid plexus tumors

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Methylation profiling of choroid plexus carcinoma cell lines

Project description:Genomic DNA was extracted from two choroid plexus carcinoma cell lines using the GeneJET genomic DNA (Thermo Fisher). DNA was quantified using the DENOVIX Fluorometer. The quality of the extracted DNA samples was assessed by the Illumina FFPE QC kit (Illumina). Bisulfite conversion of the DNA was performed using the EZ DNA methylation kit (Zymo). Bisulfite-converted DNA was hybridized to the Illumina Infinium Human Methylation EPIC array bead chip and scanned using the Illumina iScan microarray scanner (Illumina) according to the manufacturer protocol.

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Methylation profiling of pediatric choroid plexus tumors

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Gene expression data from normal mouse choroid plexus, choroid plexus papilloma and choroid plexus carcinoma

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Project description:Aggresome is a para nuclear inclusion body that functions as a storage compartment for misfolded proteins. Our previous work revealed the presence of aggresomes in pediatric choroid plexus tumors (CPT). CPTs are rare neoplasms comprised of three pathological subgroups; choroid plexus carcinoma (CPC), a grade III tumor, atypical choroid plexus papilloma (ACPP), a grade II tumor, and choroid plexus papilloma (CPP), a grade I tumor. In the current study, we aimed to investigate the prognostic value of aggresomes-positivity and its correlation to the pathological and molecular subtypes. The proteomics profiling of 21 CPT pediatric samples was investigated using ABSciex Triple TOF 5600+ mass spectrometer.

2021-02-11 | PXD021076 | Pride

Single Nucleus RNAseq dissection of choroid plexus tumor cell heterogeneity

Project description:To examine the cellular and transcriptional heterogeneity of choroid plexus tumors we determined the single nucleus transcriptomes of 23,906 nuclei from normal choroid plexus and choroid plexus tumors. The resulting cellular atlas profiles cellular and transcriptional heterogeneity, copy number alterations, and cell-cell interaction networks in normal and cancerous choroid plexus. We observe changes in choroid plexus tumor epithelial cell gene transcription that correlate with genome wide methylation profiles. In addition, we characterize tumor-grade-specific tumor microenvironments that include altered macrophage and mesenchymal cell states, as well as changes in extracellular matrix components.

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