RNA sequencing analysis of stable medulloblastoma DAOY, D425, and CHLA01 cells expressing vector only (V/O) or miR-211
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE188813 | GEO | 2023/11/01
REPOSITORIES: GEO
Similar Datasets
Project description:We deep sequenced and analyzed miRNAs using small RNA sequencing in six medulloblastoma cell lines (SHH: DAOY and ONS-76, Group 3: D341 and D425, Group 4: CHLA-01-MED and CHLA-01R-MED).
2023-12-01 | GSE240544 | GEO
Project description:The goal of this study was to profile the total proteome and transcriptome of the established medulloblastoma cell lines, Daoy and UW228, using label-free nano-LC-MS/MS-based quantitative proteomics and high-throughput RNA sequencing (RNA-Seq), coupled with pathway analysis to identify differentially expressed genes, proteins and signaling pathways with potential as prognostic markers. A total of 14250 and 12870 transcripts were detected for Daoy and UW228, respectively. Proteomic profiling identified 2630 and 1235 proteins in Daoy and UW228, representing 18% and 10% of detected transcripts, respectively. Interestingly, Daoy proteome included >50% unique proteins, while almost 90% of proteins expressed by UW228 were commonly expressed in Daoy. Differential expression of a number of adhesion, cytoskeletal and signaling molecules were observed between the two cell lines. Upregulation of a number of proteins and enrichment of key signaling pathways, including WNT, Sonic hedgehog (SHH) and integrin signaling pathways, were uniquely observed in MB cell lines, in particular in Daoy.
2017-10-27 | PXD002659 | Pride
Project description:The expression of miR-592 was found to reduce the malignant potential of Group 3 medulloblastoma cell lines, D283, D425 and HD-MB03. RNA-seq analysis was carried out to identify genes differentially expressed upon miR-592 expression in the medulloblastoma cell lines. MiR-592 expression was found to upregulate mTOR and ERK1/ERK2 signaling and bring about neuronal differentiation in D283 and D425 cells. Transcriptome sequencing was also carried out on the RNA extracted from the polyclonal population of D283 and D425 expressing miR-592 as well as the vector control population cells treated with rapamycin or U0126, a MAPK inhibitor to study if the mTOR signaling or MAPK signaling is instrumental in bringing about the neuronal differentiation.
2021-08-26 | GSE147145 | GEO
Project description:Medulloblastoma (MB) is one of the most common malignant pediatric brain tumor. The aim of our study was to understand which mechanisms are involved in aberrant activation of Wnt pathway and its association with MB tumor development. We studied the expression profiles of 19 MBs tumors using a genome-wide approach, furthermore we have included the data obtained from four independent public Datasets of gene expression (see README file below) to increase the statistical power of the study. The expression profiles identified the Wnt inhibitor gene, DKK3, significant down-regulated. DKK3 down-regulation was confirmed by qPCR in 80% of samples (27/33 MB tumors and in 3/5 MB human cell lines). Since DKK3 was found methylated in several cancers we also investigated the status of methylated CpG sites within the three promoters by a combination of two approaches: the MSP and pyrosequencing. MSP showed no methylation in all promoters while the pyrosequencing, a quantitative technique, indicated a very low level of methylation. To verify the epigenetic involvement on DKK3 silencing, we also studied the effect of Trichostatin A (TSA) in 4 MB cell lines (DAOY; D283; D425; D458). After TSA treatment we observed a significant DKK3 mRNA expression increase in 3/4 cell lines compared to the no treated cells. DAOY cells, that have a normal DKK3 expression value, did not change significantly the DKK3 expression after TSA treatment. To further validate the role of histone tail modifications as an epigenetic silencing mechanism for DKK3 in MB, we performed Chromatin Immunoprecipitation (ChIP) experiment using antibodies against acetylated histones. According to our earlier results, TSA treatment increased the signal of the histone modification meH3K4 which is related to a transcriptionally active gene respect to the untreated controls. Finally, we evaluated the DKK3 protein in three MB cell lines (DAOY; D283; D425) after 24h of TSA treatment, by immunofluorescence. We analysed 19 Medulloblastoma tumor from pediatric patients, a commercial pool (Clontech) of 24 normal cerebellum from female and male Caucasians (ages: 16-70 years; cause of death: sudden death) and a pool of 10 normal cerebellum from children (6 Caucasians and 4 African Americans; ages: 0-16 years; cause of death: sudden death) using 44K whole genome oligonucleotids microarray
2013-03-31 | E-GEOD-39182 | biostudies-arrayexpress
Project description:Using measurements of absolute protein and mRNA concentrations in cellular lysate from a Daoy medulloblastoma cell line, we quantitatively evaluate the influence of absolute transcript levels and a large number of sequence-encoded regulatory elements on steady-state human protein expression levels.
2010-02-25 | GSE20492 | GEO
Project description:Using measurements of absolute protein and mRNA concentrations in cellular lysate from a Daoy medulloblastoma cell line, we quantitatively evaluate the influence of absolute transcript levels and a large number of sequence-encoded regulatory elements on steady-state human protein expression levels. mRNA profiling: We prepared two biological replicates, each one was used in a 4-plex format array.
2010-04-22 | E-GEOD-20492 | biostudies-arrayexpress
Project description:Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is Ser/Thr protein kinase highly expressed in medulloblastoma (MB) patient samples which promotes cell migration and invasiveness downstream of growth factor receptors. Although MAP4K4 implication in the control of the membrane protrusions at the leading edge of cells during migration and invasion in MB is established, its downstream effectors governing and mediating this process in MB have not been identified. In this study we explored the proteomic neighborhood of MAP4K4 in MB cells and to identify candidate potentially affecting its activity and pro-migratory functions. Towards this aim, we expressed BioID fused versions of MAP4K4 (N- and C-terminal) in DAOY cells under presence of biotin. In the control setup, we expressed the BioID enzyme alone. After Streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions.
2022-08-04 | PXD031870 | Pride
Project description:DNase-seq on cell line Daoy (polygonal cell from 4 year old male human cerebellum, desmoplastic cerebellar medulloblastoma) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2016-12-07 | GSE90323 | GEO
Project description:Astrocytes are important cells within the medulloblastoma microenvironment. Therefore, we assessed how astrocyte secreted factors may alter Daoy (human MB cell line; ATCC HTB-186) cell gene expression.
2020-04-14 | GSE148540 | GEO
Project description:RNA sequencing of medulloblastoma cell lines DAOY and USP13-med; wild type and VAPB KO.
2023-06-28 | E-MTAB-11914 | biostudies-arrayexpress