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Transcriptomic analysis of MYC-inhibited Medulloblastoma-derived D283 Med cells

ABSTRACT: Transcriptomic analysis of MYC-inhibited Medulloblastoma-derived D283 Med cells

PROVIDER: PRJNA718454 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14102277_1.fastq.gz	Fastqsanger.gz
	SRR14102277_2.fastq.gz	Fastqsanger.gz
	SRR14102278_1.fastq.gz	Fastqsanger.gz
	SRR14102278_2.fastq.gz	Fastqsanger.gz
	SRR14102279_1.fastq.gz	Fastqsanger.gz

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Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells

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

Transcriptomic analysis of MYC-inhibited Medulloblastoma-derived D283 Med cells

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

Identification of lncMB3-dependent transcriptome in MYC-amplified D283 Med cells.

Project description:Medulloblastoma (MB) stands as the most prevalent malignant pediatric tumor affecting the central nervous system. Categorized into four primary subgroups, each with distinct biological and clinical features, MB presents unique therapeutic implications. Group 3 (G3) and 4 (G4) MBs collectively account for the majority of cases (60%) and exhibit the highest degree of aggressiveness. However, these subgroups remain poorly characterized from a biochemical perspective. Therefore, it is crucial to unveil the fundamental molecular mechanisms underlying G3 e G4 MBs to deepen our overall comprehension of these specific conditions and to pave the way for precision medicine-driven approaches. Compared to normal human cerebella, the MYC-dependent lncRNA MB3 was found to be induced in G3-derived cell lines expressing the proto-oncogene and upregulated in G3-MB primary tumors. Consistently, LncMB3 is downregulated upon MYC inhibition and in vitro studies reveal its potent anti-apoptotic activity. To dissect the molecular network through which LncMB3 operates in MB carcinogenesis, we initiated the identification of its target genes by analyzing through RNA-Sequencing the alteration of the transcriptome following LncMB3 knockdown in G3 MB cell lines, achieved through transfections of antisense Locked Nucleic Acid (LNA) oligonucleotides (GapmeRs). Here we provide the data of three polyA+ RNA samples derived from lncMB3 knockdown (KD) and 3 control samples from the MYC-amplified D283 Med cell line that were subjected to RNA-Seq analysis.

2025-09-30 | GSE277976 | GEO

Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells

Project description:Time-course hypoxia incubation (1% O2) of D283-Med medulloblastoma cells

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D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

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

Identification of lncMB3 RNA interactome through lncMB3 Native RNA Pulldown in MYC-amplified D283 Med cells.

Project description:Medulloblastoma (MB) stands as the most prevalent malignant pediatric tumor affecting the central nervous system. Categorized into four primary subgroups, each with distinct biological and clinical features, MB presents unique therapeutic implications. Group 3 (G3) and 4 (G4) MBs collectively account for the majority of cases (60%) and exhibit the highest degree of aggressiveness. However, these subgroups remain poorly characterized from a biochemical perspective. Therefore, it is crucial to unveil the fundamental molecular mechanisms underlying G3 e G4 MBs to deepen our overall comprehension of these specific conditions and to pave the way for precision medicine-driven approaches. Compared to normal human cerebella, the MYC-dependent lncRNA MB3 was found to be induced in G3-derived cell lines expressing the proto-oncogene and upregulated in G3-MB primary tumors. Consistently, LncMB3 is downregulated upon MYC inhibition and in vitro studies reveal its potent anti-apoptotic activity. To deepen the study of the LncMB3 molecular mechanism, we employed native RNA Pulldown assays followed by RNA-Sequencing to identify LncMB3 interactome. Here we provide the data of polyA+ RNA samples derived from two biological replicates of LncMB3 Native RNA Pulldown sample sets (INPUT, EVEN, ODD, LacZ) derived from the MYC-amplified D283 Med cell line that were subjected to RNA-Seq analysis.

2025-10-02 | GSE278666 | GEO

Identification of lncMB3-dependent transcriptome in MYC-amplified D283 Med cells.

Project description:Identification of lncMB3-dependent transcriptome in MYC-amplified D283 Med cells.

| PRJNA1165133 | ENA

D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

2021-06-21 | MSV000087678 | MassIVE

Identification of lncMB3 RNA interactome through lncMB3 Native RNA Pulldown in MYC-amplified D283 Med cells.

Project description:Identification of lncMB3 RNA interactome through lncMB3 Native RNA Pulldown in MYC-amplified D283 Med cells.

| PRJNA1168168 | ENA

Disseminated medulloblastoma in a child with germline BRCA2 6174delT mutation and without Fanconi anemia

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

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