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Multi-region WGS of treatment naive lung cancers

ABSTRACT: Multi-region whole-genome sequencing reveals gene-by-environment heterogeneity in metastatic lung cancer

PROVIDER: PRJEB28616 | ENA |

REPOSITORIES: ENA

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Multi-region copy-number analysis

Project description:Intra-tumour heterogeneity (ITH) foster tumour adaptation and hamper the efficiency of personalised medicine approaches. We investigated the extent of ITH within individual clear cell renal cell carcinomas (ccRCC) by multi-region sampling and copy number analysis. We analyzed 63 tumour regions and 8 normal samples from eight clear cell renal cell carcinomas using Affymetrix SNP6 arrays. All individual tumours were subjected to multi-region sampling and copy-number analysis using Affymetrix SNP6 arrays.

2013-06-04 | E-GEOD-47077 | biostudies-arrayexpress

Multi-region copy-number analysis

2013-06-04 | GSE47077 | GEO

Esophageal cancer intratumor heterogeneity revealed by multi-region whole exome sequencing and aCGH

Project description:Cancer is a disease of the genome. Many genomic abnormalities have been found in a variety of cancer types, which are believed to be attributable to tumorigenesis as well as resistance to treatment and recurrence. Genomic heterogeneity in the same type of cancer or within a tumor reveals the complexity of cancer biology so that intratumor heterogeneity has become an inherent feature of cancer. In this study, we use whole-exome sequencing and array comparative genomic hybridization technology to examine the mutational profiling and copy number changes from multi-region samples within an esophageal cancer in order to understand the genomic phylogeny in the evolution of intratumor heterogeneity in esophageal cancer.

2014-12-31 | GSE60625 | GEO

Relative spatial homogeneity revealed by transcriptional profiling of multi-region medulloblastoma samples

Project description:Affymetrix Human Gene 1.1 ST Array profiling of 52 primary, multi-region medulloblastoma samples. Total RNA was extracted from primary medulloblastoma samples and hybridized to Affymetrix Human Gene 1.1 ST Arrays (24-Array Plates) according to the manufacturer's instructions.

2015-12-31 | E-GEOD-62803 | biostudies-arrayexpress

Single-cell multi-omic and multi-region atlas of the Human Alzheimer's Disease Brain

Project description:Alzheimer’s disease (AD) is the leading cause of dementia, driven by complex molecular alterations that disrupt neural and glial cell function. However, the precise epigenomic and chromatin regulatory changes underlying AD pathogenesis across different brain regions remain incompletely understood. To address this, we generated a comprehensive single-cell multi-omic atlas of the human AD brain. We profiled 11 AD donors and 9 age-matched healthy donors, spanning three key brain regions implicated in AD pathology: the visual cortex (VC), temporal cortex (TC), and prefrontal cortex (PFC). Using single-nucleus methylome sequencing (snmC-seq3) and joint profiling of chromatin conformation and DNA methylation (snm3C-seq), we obtained extensive datasets enabling integrated analysis of transcriptional regulation, epigenetic remodeling, and 3D genome architecture. This resource allowed us to characterize AD-associated alterations in DNA methylation at promoters, enhancers, and transposable elements, as well as their consequences on transcription factor motif accessibility. At the chromatin level, we identified disease-related changes in higher-order genome organization, including compartments, topologically associating domains (TADs), and loops. By comparing multiple cortical regions, we also uncovered regional heterogeneity within matched cell types, highlighting both shared and region-specific epigenetic signatures of AD. Together, this atlas provides a systematic, multi-region view of single-cell epigenomic landscapes in AD and offers insights into regulatory mechanisms underlying disease progression.

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Relative spatial homogeneity revealed by transcriptional profiling of multi-region medulloblastoma samples

Project description:Affymetrix Human Gene 1.1 ST Array profiling of 52 primary, multi-region medulloblastoma samples.

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Single-cell multi-omic and multi-region atlas of the Aging Mouse Brain

Project description:Single-cell multi-omic and multi-region atlas of the Aging Mouse Brain

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Relative spatial heterogeneity revealed by transcriptional profiling of multi-region high-grade glioma samples

Project description:Affymetrix GeneChipÂ® Human Genome U133 Plus 2.0 Array profiling of 20 primary, multi-region high-grade glioma samples. Total RNA was extracted from primary high-grade glioma samples and hybridized to GeneChipÂ® Human Genome U133 Plus 2.0 Array according to the manufacturer's instructions.

2015-12-31 | E-GEOD-62802 | biostudies-arrayexpress

Single-cell multi-omic and multi-region atlas of the Aging Male Mouse Brain

Project description:Single-cell multi-omic and multi-region atlas of the Aging Male Mouse Brain

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Relative spatial heterogeneity revealed by transcriptional profiling of multi-region high-grade glioma samples

Project description:Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array profiling of 20 primary, multi-region high-grade glioma samples.

2015-12-31 | GSE62802 | GEO