Ontology highlight
ABSTRACT:
PROVIDER: PRJNA217773 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression profiling of melanoma brain metastases and matched extracranial metastases
| PRJNA217776 | ENA
Project description:We performed matched TCR-seq and single-cell RNA-sequencing of 5 treatment-naïve melanoma brain metastases (MBM) from 5 individual patients.
2022-07-06 | GSE200215 | GEO
Project description:Somatic copy number variation profiling in matched brain and extracranial metastases of melanoma
| PRJNA217774 | ENA
Project description:An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by mass-array genotyping, molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors. Somatic copy number variation (CNV) in 47 melanoma brain metastases (BM, except for patient 01, who had a spinal cord metastasis) and extracranial metastases (EM) were analyzed by molecular inversion probe (MIP) array (Affymetrix OncoScan FFPE Express 2.0). DNA were extracted from regions with >70% viable tumor cells from formalin-fixed and paraffin-embedded (FFPE) tissues. Of the 47 tumor samples, 22 were matched BM and EM from the same patients. In addition, 24 DNA samples from normal tissues were included as diploid controls.
2014-05-08 | E-GEOD-50495 | biostudies-arrayexpress
Project description:We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-seq and 17 snRNA-seq) from 21 patients and 10 treatment-naïve peripheral (extracranial) metastases (ECM; all snRNA-seq) from 10 patients. We performed matched spatial sequencing using SlideSeq2 (n=16) on 11 snRNA-seq samples.
2022-07-06 | GSE200278 | GEO
Project description:Genome-wide DNA methylation profiling of brain metastases from lung cancer, breast cancer, and melanoma samples. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 methylation sites in formalin-fixed paraffin-embedded (FFPE) samples from brain metastases. Samples included 30 breast cancer brain metastases, 18 lung cancer brain metastases, 37 melanoma brain metastases, and 4 samples with brain metastases from patients with uncertain primary.
2018-08-28 | GSE108576 | GEO
Project description:An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors. Seventy-two samples from 52 brain (except for patient 01, who had a spinal cord metastasis) and extracranial metastases of melanoma were analyzed. Available biological replicates (different parts of the same tumor) were included.
2014-05-08 | E-GEOD-50493 | biostudies-arrayexpress
Project description:Bulk ATAC-seq on 24 patient-derived cell lines corresponding to 4 melanoma brain metastases (MBM) and 4 peripheral/extracranial melanoma metastses (ECM).
2022-07-06 | GSE205033 | GEO
Project description:An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by mass-array genotyping, molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors.
2014-05-08 | GSE50495 | GEO
Project description:Melanoma is one of the most aggressive and treatment-resistant cancers. It represents the most life-threatening neoplasm of the skin, and its incidence has been increasing for the last three decades. Melanoma evolves from the local transformation of melanocytes to primary tumors, which can metastasize to multiple organs. Brain metastases represent one of the most significant causes of death in cutaneous melanoma patients. Despite aggressive multi-modality threapy, patients with melanoma brain metastasis have a median survival of less than a year, with a majority of these patients dying as a result of their intracranial disease. To identify alterations in gene expression related to brain metastasis, we used Affymetrix expression arrays to assess differentially expressed genes in melanocytes, lymph node metastases, and brain metastases. Total RNA from twenty-two specimens representing normal melanocytes (n=3), melanoma lymph node metastasis (n=12), and melanoma brain metastasis (n=7) was extracted and analyzed by Affymetrix expression arrays. Melanocytes specimens were used as control samples. Melanocytes were acquired from Invitrogen (LifeTechnologies). Metastatic melanoma specimens were taken from different patients, established as cell lines in the John Wayne Cancer Institute. Early passages (less than 6) were used to perform expression analysis.
2013-09-19 | E-GEOD-44660 | biostudies-arrayexpress