Similar Datasets
Project description:Normal brain RNAseq data provides a critical comparitor for evaluation of gene expression changes in childhood brain tumors.
2024-02-05 | GSE244124 | GEO
Project description:<p>Francesca Petralia,Nicole Tignor,Boris Reva, et al., (2020) <a href="https://www.cell.com/cell/fulltext/S0092-8674(20)31451-3" target="_blank">Cell 183, 1962-1985</a></p><p>We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.</p><p>The Children's Brain Tumor Network (CBTN) and the Pacific Pediatric Neuro-Oncology Consortia (PNOC) are collaborative research consortia focused on identifying therapies for children with brain tumors (<a href="https://cbttc.org" target="_blank">https://cbttc.org</a>). The consortia have contributed a <a href="https://kidsfirstdrc.org/support/studies-and-access/#SD_BHJXBDQK" target="_blank">Pediatric Brain Tumor Atlas (PBTA) dataset</a>, a cohort of 991 brain tumor subject clinical data, with associated whole genome sequencing and RNAseq hosted by the Gabriella Miller Kids First Data Resource (<a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>) as part of the Gabriella Miller Kids First Pediatric Research Program (Kids First). Kids First is a Pan NIH Common Fund program dedicated to the development of large-scale data resources to help researchers uncover new insights into the biology of childhood cancer and structural birth defects (<a href="https://commonfund.nih.gov/KidsFirst" target="_blank">https://commonfund.nih.gov/KidsFirst</a>).</p><p>Mass Spectrometry raw data generation along with preliminary analyses were performed at the <a href="https://tcmp.hms.harvard.edu/" target="_blank">Thermo Fisher Scientific Center for Multiplexed Proteomics (TCMP)</a>, Harvard Medical School (HMS) under the direction of <a href="https://cellbio.med.harvard.edu/people/faculty/gygi" target="_blank">Prof. Steven Gygi</a>. Samples were prepared using the streamline (SL)-TMT protocol (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994137/" target="_blank">Navarrete-Perea et al., 2018</a>) and MS analysis was performed using the SPS-MS3 strategy (<a href="https://www.nature.com/articles/nmeth.1714" target="_blank">Ting et al., 2011</a>) developed in the <a href="https://gygi.med.harvard.edu/" target="_blank">Gygi lab</a>. Additional data analyses from the CPTAC Common Data Analysis Pipeline (<a href="https://www.ncbi.nlm.nih.gov/pubmed/26860878" target="_blank">Rudnick et al., 2016</a>) and from the University of Michigan Proteomics and Integrative Bioinformatics Laboratory (<a href="https://github.com/Nesvilab" target="_blank">https://github.com/Nesvilab</a>) are also provided. All raw and processed genomic data, as well as pathology reports, radiology reports, MRIs, histology slide images are accessible via the <a href="https://portal.kidsfirstdrc.org/dashboard" target="_blank">Kids First DRC (Data Resource Center)</a>.</p>
2021-02-04 | MSV000086810 | MassIVE
Project description:The central nervous system (CNS) is a common site of metastatic disease in patients with breast cancer and has few therapeutic options with dismal outcomes. The purpose of our study was to identify common and rare events that underlie breast cancer CNS metastasis. We performed deep genomic profiling, which integrated gene copy number, gene expression and DNA methylation datasets on a collection of breast brain metastases. We identified frequent large chromosomal gains in 1q, 5p, 8q, 11q, and 20q and frequent broad level deletions involving 8p, 17p, 21p and Xq. Frequently amplified and overexpressed genes included ATAD2, BRAF, DERL1, DNMTRB and NEK2A. The ATM, CRYAB and HSPB2 genes were commonly deleted and underexpressed. Knowledge mining revealed enrichment in cell cycle and G2/M transition pathways, which contained AURKA, AURKB and FOXM1. Using the PAM50 breast cancer intrinsic classifier, Luminal B, Her2+/ER negative, and basal-like tumors were identified as the most commonly represented breast cancer subtypes in our CNS metastasis cohort. While overall methylation levels were increased in breast cancer CNS metastasis, basal-like CNS metastases were associated with significantly lower levels of methylation. Integrating DNA methylation data with gene expression revealed defects in cell migration and adhesion due to hypermethylation and downregulation of PENK, EDN3, and ITGAM. Hypomethylation and upregulation of KRT8 likely affects adhesion and permeability. Genomic and epigenomic profiling of breast CNS metastasis has provided insight into the somatic events underlying this disease, which have potential in forming the basis of future therapeutic strategies. Three sample-types: 35 Breast Brain Metastasis samples, 10 Non-Neoplastic Brain samples, and 10 Non-Neoplastic Breast samples.
2014-03-13 | E-GEOD-52604 | biostudies-arrayexpress
Project description:RNAseq of human brain cell lines
| PRJNA672108 | ENA
Project description:The characteristics of immune cells infiltrating pediatric brain tumors is largely unexplored. A better understanding of these characteristics will provide a foundation for development of immunotherapy for pediatric brain tumors. Gene expression profiles were used to identify immune marker gene that are differentially expressed between various brain tumor types. Gene expression profiles were generated from surgical tumor and normal brain samples (n=130) using Affymetrix HG-U133plus2 chips (Platform GPL570). Gene expression profiles of different types of brain tumors and normal brain were filtered to obtain gene expression of key immune cell markers. Comparative analyses between different brain tumors and normal brain was used to identifiy differential immune characteristics of these tumors.
2013-08-25 | E-GEOD-50161 | biostudies-arrayexpress
Project description:Posterior fossa subgroup A (PFA) ependymoma is a brain tumor of childhood with a high rate of recurrence. Here we have performed RNAseq on a longitudinal cohort of patient samples obtained at presentation and at recurrence(s), in order to identify the biological correlates of treatment failure and tumor evolution.
2023-06-01 | GSE226957 | GEO
Project description:Brain RNAseq, comparing wild type and Sgo1 mouse (all 24 months of age)
2018-07-31 | GSE115185 | GEO
Project description:Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from four subtypes of MB patients. We find highly concordance of DNA methylation between CSF ctDNA and tumor DNA in a subtype manner. Our results show that CSF ctNDA methylation can be a minimal invasive precisely method to assess epigenetic alterations of MB in a subtype manner, which is complementary to current diagnoses of MB tumors.
2023-06-01 | GSE178169 | GEO
Project description:We used single-cell RNAseq to investigate the heterogeneity of glioblastoma tumors and assess differential expression between cells within and in proximity of the tumor.
2017-11-01 | GSE84465 | GEO
Project description:The characteristics of immune cells infiltrating pediatric brain tumors is largely unexplored. A better understanding of these characteristics will provide a foundation for development of immunotherapy for pediatric brain tumors. Gene expression profiles were used to identify immune marker gene that are differentially expressed between various brain tumor types.
2013-08-25 | GSE50161 | GEO