Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells
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PROVIDER: PRJNA418498 | ENA |
REPOSITORIES: ENA
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Project description:Elucidation of the impact of hypoxia in D283-Med (medulloblastoma Homo sapiens, human, ATCC® HTB-185™) cells to depict molecular mechanisms, which could explain drug resistance when cells are exposed to long-term hypoxia (5 days). Global gene expression study by microarray analysis to allow an efficient search for a range of genes. D283-MED cells were incubated for a varied hypoxic duration (0, 6, 64 and 96 hours in triplicate), cDNA samples were prepared and sent directly to NimbleGen.
2017-11-16 | GSE106959 | GEO
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Project description:Medulloblastoma is one of the most common malignant pediatric brain tumors. Group 3 is the most aggressive molecular subgroup, showing the highest rate of metastasis at diagnosis. To date, very few long noncoding RNAs have been implicated in Group 3 Medulloblastoma biology. Here, we identified the long noncoding RNAs dependent on the activity of the MYC oncogene, the major driver gene of Group 3 Medulloblastoma.
2021-08-11 | GSE171117 | GEO
Project description:We describe an 8 year old child who had disseminated anaplastic medulloblastoma and a deleterious heterozygous BRCA2 6174delT germline mutation. Molecular profiling was consistent with Group 4 medulloblastoma. The posterior fossa mass was resected and the patient received intensive chemotherapy and craniospinal irradiation. Despite this, the patient succumbed to a second recurrence of his medulloblastoma, which presented eight months after diagnosis as malignant pleural and peritoneal effusions. Continuous medulloblastoma cell lines were isolated from the original tumor (CHLA-01-MED) and the malignant pleural effusion (CHLA-01R-MED). Here we provide their analyses, including in vitro and in vivo growth, drug sensitivity, comparative genomic hybridization and next generation sequencing analysis. In addition to the BRCA2 6174delT, the medulloblastoma cells had amplification of MYC, deletion at Xp11.2 and isochromosome 17, but no structural variations or overexpression of GFI1 or GFI1B. To our knowledge, this is the first pair of diagnosis/recurrence medulloblastoma cell lines, the only medulloblastoma cell lines with BRCA2 6174delT described to date, and the first reported case of a child with medulloblastoma associated with a germline BRCA2 6174delT who did not also have Fanconi anemia. Continuous medulloblastoma cell lines were isolated from the original tumor (CHLA-01-MED) and the malignant pleural effusion (CHLA-01R-MED). Here we provide their analyses, including in vitro and in vivo growth, drug sensitivity, comparative genomic hybridization with Agilent 400k CGH arrays and whole transcriptome RNASeq analysis.
2015-07-06 | E-GEOD-70003 | biostudies-arrayexpress
Project description:We describe an 8 year old child who had disseminated anaplastic medulloblastoma and a deleterious heterozygous BRCA2 6174delT germline mutation. Molecular profiling was consistent with Group 4 medulloblastoma. The posterior fossa mass was resected and the patient received intensive chemotherapy and craniospinal irradiation. Despite this, the patient succumbed to a second recurrence of his medulloblastoma, which presented eight months after diagnosis as malignant pleural and peritoneal effusions. Continuous medulloblastoma cell lines were isolated from the original tumor (CHLA-01-MED) and the malignant pleural effusion (CHLA-01R-MED). Here we provide their analyses, including in vitro and in vivo growth, drug sensitivity, comparative genomic hybridization and next generation sequencing analysis. In addition to the BRCA2 6174delT, the medulloblastoma cells had amplification of MYC, deletion at Xp11.2 and isochromosome 17, but no structural variations or overexpression of GFI1 or GFI1B. To our knowledge, this is the first pair of diagnosis/recurrence medulloblastoma cell lines, the only medulloblastoma cell lines with BRCA2 6174delT described to date, and the first reported case of a child with medulloblastoma associated with a germline BRCA2 6174delT who did not also have Fanconi anemia.
2015-07-06 | GSE70003 | GEO
Project description:Our goal is the identification of more and more missing proteins from cancer cell lines. This project focuses on D283 med and U-118mg cell lines which contribute to 12 missing protein identification.
2020-11-26 | PXD021482 | Pride
Project description:Medulloblastoma is subdivided into different subgroups: WNt, SHH, Group 3 and Group 4. Since these subgroups are associated with different OS and metastasis rates it is crucial to understand them better. Six medulloblastoma cell lines, DAOY, ONS-76, D458, HD-MB03, CHLA-01-MED, CHLA-01R-MED, have been sequenced to compare them with medulloblastoma patient data. Methods: Medulloblastoma cell lines representating the different subgroups have been cultured and cell were harvested and RNA was isolated when 70% confluency was reached. In detail, DAOY and D458 were grown in DMEM (Thermo Fisher) with 10% FBS (HyClone, Thermo Fisher), ONS-76 and HD-MB03 were grown in RPMI 1640 (Sigma-Aldrich) with 10% FBS and CHLA-01-MED and CHLA-01R-MED were grown in DMEMF12 supplemented with B27, 20 ng/ml EGF and 20 ng/ml bFGF (all Thermo Fisher). All cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2. During the course of this study, all cell lines were routinely confirmed to be mycoplasma negative (MycoAlert, Lonza, Basel, Switzerland).Cell pellets of at least 100,000 cells were washed with HBSS and frozen in liquid nitrogen. For homogenization, ceramic spheres (Lysing Matrix D, MP Biomedicals, Santa Ana, California, USA) and the FastPrep-24 homogenizer was used (MP Biomedicals, speed 4 m/s, tube holder MP:24*2 and time 20 s). Total RNA was isolated from 2D pellets using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. In total, 3 biological replicates of each cell line were processed respectively. RNA amount was determined using the Qubit RNA BR kit with the Qubit 4 (both ThermoFisher). Library preparation and RNA sequencing (transcriptome sequencing including lncRNA on Illumina PE150) were performed by Novogene (Cambridge, UK) Company Limited, Cambridge, UK. Samples with less than 100 ng or with non-qualifying RIN values were excluded from the sequencing. All prepared libraries successfully passed Novogene’s internal quality control checks and were sequenced. Following sequencing, quality control of the sequencing data was performed that confirmed all samples had high quality scores, indicating good technical performance of the sequencing. We used FastQC to perform quality checks of raw RNA data followed by adapter and low quality read filtering using the Cutadapt package (version 1.16.6) [reference]. The trimmed paired-end sequences were aligned with the human genome (hg38) and Gencode annotation (v35) using the STAR (version 2.7.5b) alignment tool. Unique reads from genomic alignment were processed and we used the featureCount tool for transcript abundance quantification. STAR read counts were used as input into edgeR. Genes with read counts greater than 10 in three or more samples were kept for subsequent analyses. After normalization analyses, counts per million (cpm) on a log2 scale were used for downstream exploratory analyses.
2022-03-02 | E-MTAB-9823 | biostudies-arrayexpress